Evaluation Of Genetic Resources And Development Of Specific Molecular Identity Of "Yufen 1" H Line

The matching line of the “Yufen 1” layer was authorized by the National Commission on Livestock and Poultry Genetic Resource in 2015.As the progenitor,line H is characterized by early sexual maturity,a fast plumage line,high egg production,and a Columbian feather pattern.Protecting its genetic uniqueness is the core of the breeding work.With the breeding of new poultry breed lines,the identification of breeds and the development of molecular IDs for different breeds is a major challenge that needs to be solved.At present,there is no relevant method for the identification of germplasm specific to the "Yufen 1" H line(YF).Therefore,to accurately assess the genetic diversity and population structure of poultry populations,establish a simple,economic,accurate and efficient breed identification system,and construct breedspecific molecular ID cards is a powerful measure to combat counterfeit breeds and reasonably protect and utilize indigenous breed resources.Herein,this study systematically explored the genetic diversity and population structure of YF by the whole genome resequencing of YF,combined with the published whole-genome resequencing data of two commercial chicken breeds,11 Chinese indigenous chicken breeds,and 1 wild chicken breed.Moreover,this study constructed a specific molecular identify card for YF,which can be used for the authenticity identification of YF,and provide a scientific and powerful basis for the identification and protection of germplasm resources of YF.Research 1: Genetic Resources Evaluation of “Yufen 1” H Line Chickens Based on WholeGenome Resequence DataIn this study,the whole genome of 60 YF was resequenced,and a total of 1.28 Tb of clean data was obtained.The comparison rate of clean data to reference genome was more than 99%,and the average coverage depth of individuals was more than 17.03×.The genetic variation information of YF was examined,and 12,503,541 SNPs were obtained.The genetic diversity parameters such as minor Allele frequency(MAF),observed heterozygosity(Ho),nucleotide diversity(π),expected heterozygosity(He),effective population size(Ne)and inbreeding coefficient(FROH)of 15 chicken breeds were analyzed,and it was found that the genetic diversity of YF was lower than that of other Chinese indigenous chicken breeds and higher than commercial chicken breeds,and the population uniformity is better.The results of the linkage disequilibrium decay analysis showed that the decay rate of YF was significantly slower than that of the other 11 Chinese indigenous chicken breeds.These results suggested that the YF population may have been subjected to more intensive artificial selection during intensive breeds.Moreover,a principal component analysis,a neighbor-joining tree analysis,a structure analysis,and genetic differentiation indices indicated that YF harbors a distinctive genetic resource with a unique genetic structure separate from that of Chinese indigenous breeds at the genome level.Research 2: Development and application of specific molecular identity molecular IDs of “Yufen 1”H lineIn this study,a selective sweep analysis was performed between high-yielding hens(WLH,RIR and YF)and non-high-yielding hens(Chinese indigenous chicken breeds and RJF).1124 selected regions in high-yielding hens were screened,and 526 genes were annotated.Functional enrichment analysis and literature review revealed that PIK3 CA,MAD2L1,CPEB3,RAF1 and MAPK3 are possible candidates for influencing reproductive performance in poultry.Another selective sweep analysis was carried out between YF and NYF,1140 selected regions in YF were screened.SNPs were extracted from the selected region of YF,and the authenticity of the specific SNPs was initially verified by PCR amplification and Sanger sequencing.The KASP typing technology platform was used to verify the typing of 234 samples from 7 chicken breeds,and finally 6 specific SNPs molecular markers(Chr9:13723265,Chr9:13745245,Chr9:13795646,Chr9:13798154,Chr2:45509616,Chr2.45510792)were used as molecular IDs for the YF.Also,6 specific SNPs were applied to Sanger sequencing to identify this line,and more satisfactory results were obtained.In the process of identification and evaluation of YF,only 6 specific SNPs genotypes of this line were compared to determine whether it is YF.In conclusion,the genetic variation information of YF was detected at the whole genome level in this study,and the genetic diversity and population structure of YF were comprehensively studied.Using selective sweep analysis and KASP typing technique,the specific molecular IDs of YF was constructed,which provided a scientific and powerful basis for the identification and protection of YF.This study is beneficial to the germplasm resources development of YF.