| Duck meat is one important source of poultry meat and has a great market demand.Therefore,increasing the body size and breast meat yield is still one key objective in duck breeding.However,with the continuous application of traditional breeding methods,the breeding improvement of body and breast meat has become more and more difficult.Meanwhile,due to the diversity of Chinese food culture,the breeding for high duck neck yield is also meaningful.However,the measurement of duck neck yield in vivo is difficult to achieve,making the breeding for high neck yield difficult.Vertebra number variation widely existed in domestic animals.The increase of vertebra number could enlarge body size and increase meat yield.Along with the development of genetic resequencing technology and analytical technology,the main QTLs affecting the thoracic and lumbar vertebra number has been discovered in pigs,which provided an effective molecular marker for enlarging body size and improving meat yield of pigs.However,study on vertebra number variation in ducks has not been reported yet.Therefore,studying vertebra number variation in duck population and exploring genetics loci affecting vertebra number variation has important theory and application value.In this study,we studied the vertebra number variation through X-ray technology,making skeleton specimen and other methods in several duck populations including Pekin duck,mallard,and Pekin duck ×mallard F2 population,respectively.The cervical vertebra number(CVN),thoracic vertebra number(TVN),body weight(BW),body length(BL),neck length(NL),neck weight(NW),neck percentage(NWP),breast meat weight(BMW),keel length(KL)and breast meat percentage(BMWP)of 405 F2 ducks were recorded at 49 week of age.Then we explored the effects of vertebra number on economic traits using quantitative genetic analysis.Single nucleotide polymorphism(SNP)and copy number variation(CNV)across the genome were detected with GATK workflow and CNV caller using Next generation sequencing(NGS)data of 405 F2 ducks and 125 commercial Pekin ducks.Using the two kind of genetic variants,in combination of phenotypic data,genome-wide association study was performed using EMMAX and TASSEL program to find the main QTLs and genes affecting the vertebra number variation and other economic traits,and to provide corresponding theoretical basis and molecular markers for future duck breeding.The main results of the study are as follows:1.Morphologic research on spine of ducksBy sensing the transverse process of cervical vertebras of peeled ducks,in combination with skeleton specimen making,the cervical vertebras can be quickly and accurately counted.And by counting the duck ribs,the thoracic vertebras can be quickly and accurately counted.The duck spine consists of cervical vertebrae,thoracic vertebrae,lumbar vertebrae,sacral vertebra and caudal vertebrae.There exited abundant variations in the shape and number of each part of the vertebra.The latter several thoracic vertebras were highly integrated with the lumbar and sacral vertebrae,and there were variations in the degree of thoracic vertebra healing in the duck population.Lumbar vertebra number and sacral vertebra number were difficult to count due to high healing.2.Study on vertebra number variation in duck populationsThere exits cervical and thoracic vertebra number variation in duck populations.The ducks with 14 or 16 cervical vertebras in duck populations were rare variations.In the Pekin duck,mallard,and Pekin duck × mallard F2 populations,most ducks have 15 cervical vertebras,a few ducks have 14 or 16 ducks.The thoracic vertebra number of ducks is usually 9 or 10.A few ducks with 11 thoracic vertebras were observed in Pekin duck breeding population.The percentage of ducks with different cervical and thoracic vertebras showed difference between different sexes,between mallard population and Pekin duck population,and between Pekin duck populations.3.Influence of cervical and thoracic vertebra number on slaughter traits in ducksThe heritability estimates for CVN,TVN,BL,BW,NL,NW,NC,NL/BL,NWP,KL,BMW,and BMWP were 0.08,0.65,0.49,0.47,0.36,0.45,0.38,0.18,0.43,0.55,0.40 and 0.48,respectively.CVN had relatively high genetic and phenotypic correlation with NL(0.40 and0.29),NW(0.13 and 0.17)and NWP(0.23 and 0.19).In contrast with CVN,TVN showed low genetic and phenotypic correlation with KL(0.01 and 0.05)and BMWP(0.03 and-0.05).While genetic and phenotypic correlations of KL with BMW(0.72 and 0.49)and BMWP(0.11 and0.32)were positive and high.The results indicated that selection on cervical vertebra number could improve the neck yield indirectly,while selection on thoracic vertebra number could not increase the yield of the breast meat.Besides that,the study also verified that the selection on keel length could improve breast meat yield.4.Genome-wide SNP-association study on cervical and thoracic vertebra related traitsBased on genome-wide SNP information and phenotypic data of 405 Pekin duck ×mallard F2 ducks and 125 commercial Pekin ducks,we conducted genome-wide association study on cervical and thoracic vertebra related traits.No SNP was found to be significantly associated with cervical and thoracic vertebra related traits.SNPs around IGF2BP1 gene were found to be significantly associated with body weight,body length,neck weight,neck length,neck circumference,breast meat weight and keel length.After the causative mutation in IGF2BP1 reported previously fixed,there still existed SNPs associated with body length,neck length and keel length.The HOX gene family members might be candidate genes for body length,neck length and keel length.5.Genome-wide CNV-association study on cervical and thoracic vertebra related traitsUsing the NGS data of 125 commercial Pekin ducks,we detected 9431 copy number variation regions with an average length of 4677 bp based on the read depth.Among all the 9431 CNVRs,2123 of them were located in uncharacterized chromosome.589 CNVRs with high quality located on autosomes were used for GWAS analysis.6 CNVRs were detected to be significantly associated with cervical vertebra number,which were located on chr5,chr7,chr9,chr10 and chr19.In the significantly associated CNV region on chr7,there exited two genes named WNT10 A and WNT6 which belong to WNT gene family.The WNT gene family involved in several embryologic development processes,including regulation of cell fate and patterning during embryogenesis.In conclusion,there existed cervical and thoracic vertebra number variation which varied in different populations and sexes.The improvement on cervical vertebra number could improve neck yield and the improvement on thoracic vertebra number could not improve breast meat yield.Genome-wide SNP association study found SNPs around Hox B might influence the body length,neck length and keel length.Genome-wide CNV association study found 6 CNVs significantly associated with cervical vertebra number.In this study,vertebra number variations and their effect on the production traits of ducks were systematically investigated in several duck populations,and GWAS on the related traits was carried out,which provided a theoretical basis for the duck neck and breast meat breeding,and laid a research foundation for the study on duck vertebra number variation. |
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