Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig

Background As pre-cut and pre-packaged chilled meat becomes increasingly popular,integrating the carcasscutting process into the pig industry chain has become a trend.Identifying quantitative trait loci(QTLs)of pork cuts would facilitate the selection of pigs with a higher overall value.However,previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts,neglecting the investigation of QTLs influencing these traits.This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips.Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values(GEBVs)for pork cuts.Results We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes,respectively.Specifically,we found that HMGA1,VRTN and BMP2 were associated with body length and weight.Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones,VRTN primarily affects the number of vertebrates,and BMP2 primarily affects the length of vertebrae and the size of hind leg bones.The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population,divided by the square root of the trait’s heritability.The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693.Notably,ribs,boneless picnic shoulder,tenderloin,hind leg bones,and scapula bones exhibited prediction accuracies exceeding 0.600.Employing better models,increasing marker density through genotype imputation,and pre-selecting markers significantly improved the prediction accuracy of GEBVs.Conclusions We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes.These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection.Additionally,we have constructed the first reference populations for genomic selection of pork cuts in pigs.

Genome-wide and candidate gene association studies identify BnPAP17 as conferring the utilization of organic phosphorus in oilseed rape

Phosphorus(P)is essential for living plants,and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide.As the most important organ for plants,root morphology traits(RMTs)play a key role in P absorption.To investigate the genetic variability of RMT under low P availability,we dissected the genetic structure of RMTs by genome-wide association studies(GWAS),linkage mapping and candidate gene association studies(CGAS).A total of 52 suggestive loci were associated with RMTs under P stress conditions in 405 oilseed rape accessions.The purple acid phosphatase gene BnPAP17 was found to control the lateral root number(LRN)and root dry weight(RDW)under low P stress.The expression of BnPAP17 was increased in shoot tissue in P-efficient cultivars compared to root tissue and P-inefficient cultivars in response to low P stress.Moreover,the haplotype of BnPAP17^(Hap3)was detected for the selective breeding of P efficiency in oilseed rape.Over-expression of the BnPAP17^(Hap3)could promote the shoot and root growth with enhanced tolerance to low P stress and organic phosphorus(Po)utilization in oilseed rape.Collectively,these findings increase our understanding of the mechanisms underlying BnPAP17-mediated low P stress tolerance in oilseed rape.

Genetic Parameters for Udder Traits in Slovak Dairy Sheep and Their Crosses with Specialized Breeds

Genetic parameters for udder morphology traits either subjectively assessed or exactly measured, and a combination of both sets of traits were estimated using multi-trait animal model and algorithm REML （program VCE 4.0）. Purebred Tsigai and Improved Valaehian breeds, and crossbreds with Lacaune and East Friesian were studied. Subjectively assessed traits included udder depth （UD）, cistern depth （CD）, teat placement （TP）, teat size （TS）, udder cleft （UC）, udder attachment （UA） and udder shape （US）. Exact measurements included udder length （UL）, udder width （UW）, udder depth （UDEx）, cistern depth （CDEx）, teat length （TL） and teat angle （TA）. Heritabilities estimated for subjectively assessed traits were lower than those estimated for exact measurements and ranged from 0.090 （UA） to 0.294 （CD）. Heritabilities estimated for exact measurements ranged from 0.102 （UW） to 0.448 （CDEx）. In simultaneous evaluation of four subjectively assessed traits and corresponding exact measurements, heritabilities remained almost the same. High genetic correlations （0.855 to 0.937） between UD and UDEx, CD and CDEx, TS and TL and between TP and TA were found. These findings allow presuming that genetic evaluation based on subjectively assessed traits could become an effective tool in selection programs aimed at improvement of udder morphology in dairy ewes.

Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency

Maize（Zea mays L.） root morphology exhibits a high degree of phenotypic plasticity to nitrogen（N） de ficiency,but the underlying genetic architecture remains to be investigated Using an advanced BC_4F_3 population,we investigated the root growth plasticity under two contrasted N levels and identi fied the quantitative trait loci（QTLs） with QTL-environment（Q×E）interaction effects. Principal components analysis（PCA） on changes of root traits to N de ficiency（D LN-HN） showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC,while root traits scattered highly on PC_2 and PC_3. Hierarchical cluster analysis on traits for D LN-HN further assigned the BC_4F_3 lines into six groups,in which the special phenotypic responses to N de ficiency was presented These results revealed the complicated root plasticity of maize in response to N de ficiency that can be caused by genotype environment（G×E） interactions. Furthermore,QTL mapping using a multi-environment analysis identi fied 35 QTLs for root traits. Nine of these QTLs exhibited signi ficant Q×E interaction effects. Taken together,our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N de ficiency,which will be useful for developing maize tolerance cultivars to N de ficiency.