genetic and genomic features for russian simmental cattle ......blupf90, plink 1.90, splitstree...

Genetic and genomic features for Russian Simmental cattle different ancestry derived by SNP data

Sermyagin A.A.1, Ignatieva L.P.1, Dotsev A.V.1, Zimina A.A.1, Mészáros G.2, Soelkner J.2, Brem G.3, Zinovieva N.A.1

1L.K. Ernst Federal Research Center for Animal Husbandry, Moscow region, Russia / 2University of Natural Resources and Life Sciences, Vienna, Austria/ 3Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria.

Abstract

The population of Simmentalcattle in Russia has a third placeacross country for breedingresources. It is most popularbreed for southeast of Russiacentral part, Volga region, Uraland Altai. The aim of this studywas to clarify a geneticrelatedness for Simmental cattleRussian and Western Europeorigin in connection withpopulation structure using SNPdata and possibilities of genomicselection.

Material and Methods ResultsBy Animal Model approach for pedigree

and offspring data, estimated breedingvalues of 669 sires revealed the highestranking in HOL (+57.0 kg of milk), followedby RUS/FLV (-15.4 kg) and lowest in RSB (-69.4 kg) for assessing at Simmental herds.The heritability for milk traits ranged from0.140 to 0.194, for days open - 0.061, forbody weight - 0.073. MDS and Neighbor-Net analyses revealed the clear clusteringby ancestry of all the studied animals.More distant from HOL was RUS(Fst=0.129), further FLV (Fst=0.127), SCH(Fst=0.112) and RSB (Fst=0.057). Simmentalgroups of animals formed the commoncluster with closest distances betweenRUS, FLV and SCH (Fst=0.023-0.029). ForRSB it was more (Fst=0.040-0.056). GWASanalysis proved significant associationswith p-value 10-4-10-6 on chromosomesfor milk yield (BTA3, 21, 29), fat (BTA8, 9,14, 17, 20) and protein percentage (BTA 3,5, 6, 15, 24).

Conclusion

LD analysis showed (ranged bychromosomes within 0.139...0.212)that the RSB, SCH, FLV and RUSpopulations can be used as aconsolidated reference group toenhance possibilities for predictinggenomic EBVs.

Also in the framework of thisexamine the studies to find genomepatterns regions for signatures ofselection in two Russian Simmentalpopulations different origin will becontinue.

Supported by RFBR №17-29-08030 and

MSHERF №0445-2019-0027

For genotyping we used 50K(Illumina) and 150K (Neogen)BeadCheap platforms. After qualitycheck control were taken intoanalysis 37143 SNPs. The trainingdataset for genomic data included268 bulls: Russian Simmentalancestry (RUS, 35), WesternSimmental ancestry (Austrian andGerman, FLV, 130), Sychev breed(SCH, 29), Russian Red Spotted breed(Simmental with a differentproportion of Holstein genes, RSB,58) and Holstein as the outgroup(HOL, 16). BLUPF90, Plink 1.90,SplitsTree 4.14.6, R-package StAMPPsoftware were used.

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Material and Methods

References:• Misztal, I. BLUPF90 and related programs (BGF90). Proceedings of the 7th world congress on genetics applied to

livestock production / I. Misztal, S. Tsruta, T. Strabel, B. Auvray, T. Druet, D.H. Lee. Montpellier, CommunicationNo. 28-27. 2002. V. 28. - P. 21-22.

• Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ,Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J HumGenet. 2007;81:559-575.

• Keenan K, McGinnity P, Cross TF, Crozier WW, Prodohl PA. diveRsity: An R package for the estimation ofpopulation genetics parameters and their associated errors. Methods in Ecology and Evolution. 2013;4:782-788.

Biodiversity analysis DNA extraction:

• For the purposes of this paper the Western or Fleckvieh Simmental cattle means animals with Austrian or German origin. The Russian Simmental population includes animals that have a common national breeding program and own genealogical structure from 1950s to present. The sperm samples from bulls were provided by the six AI stations located in European Russia, Siberia.

• Genomic DNA was extracted using Nexttec column (Nexttec Biotechnology GmbH, Germany). The DNA concentration was not less than 260 nm.

Genotyping:

• 268 purebred Simmental different origin and Sychev bulls, crossbred Simmental×Holstein bulls using the Illumina Bovine SNP50 v2, GGP 150K BeadChip were genotyped (selected 37143 SNPs, Plink 1.9);

• Russian Simmental (RUS, n=35);

• European Fleckvieh (Western Simmental) (FLV, n=130);

• Simmental improved by Holsteins, Russian Red Spotted breed (RSB, n=58);

• Holsteins purebred as the outgroup (HOL, n=16).

• 14 regions, 42 breeding herds in Russia were took into account for studying.

Software:

• BLUPF90, PLINK 1.07, SplitsTree 4.14.5 software and R package “diveRsity ” (StAMMP) were used to perform the statistical analyses.

• Quality control for genotyping data was: mind – 0.1, geno – 0.1, maf – 0.05, indep-pairwise – 50|5|0.5

Population HOLSTEIN SYCHEV FLECKVIEHRUSSIAN RED

SPOTTED RUSSIAN

SIMMENTAL

HOLSTEIN - - - - -SYCHEV 0,112 - - - -FLECKVIEH 0,127 0,029 - - -RUSSIAN RED

SPOTTED 0,057 0,040 0,056 - -

RUSSIAN

SIMMENTAL 0,129 0,023 0,024 0,054 -

Table 1. Genetic distances between breed populationsby F-statistics (Fst)

Multi-dimensional scaling of genomic variability in Russian

Simmental cattle population:

HOLSTEIN (outgroup),

SICH – Sychev breed (Smolensk region),

SIM_FLKV – European Fleckvieh (Western Simmental,

Germany / Austria) ,

SIM_HOL – Simmental improved by Holsteins, Russian Red

Spotted breed,

SIM_RUS - Russian Simmental origin.

Neighbor-Net dendrogram constructed from pairwise matrix of FST values

Individual Neighbor-Net tree by IBS for different Simmental and related cattle populations in Russia

(Holsteins as the outgroup population)

TraitsHolstein breed,

n=108 bulls

Simmental breed, n=530

bulls

Russian Red Spotted breed,

n=31 bullsEBV rel, % EBV rel, % EBV rel, %

305-milk yield, kg

+57,0 70,9 -15,4 70,7 -69,4 67,3

Fat milk, kg +1,68 71,8 -0,51 71,6 -2,03 68,4

Fat percentage, %

-0,010 63,6 +0,0004 63,5 +0,014 59,6

Protein milk, kg +1,63 71,0 -0,86 70,8 -2,40 67,4

Protein percentage, %

+0,0003 66,2 -0,005 66,0 +0,001 62,1

Days open +2,36 45,5 -1,23 45,8 -0,53 41,1

Number of daughters(min / max)

-72

(10 / 445)

-92

(10 / 1500)

-56

(10 / 304)

Heritability (on the diagonal) and genetic correlations

for the common dataset in studied population

Traits NI DO BW305-MY

FM FP PM PP

Number per insemination

0,073

Days open -0,049 0,061

Body weight 0,050 0,196 0,163

305-milk yield

0,125 0,249 0,229 0,180

Fat milk 0,130 0,263 0,230 0,977 0,194

Fatpercentage

0,071 0,106 0,058 0,149 0,350 0,142

Proteinmilk

0,130 0,251 0,255 0,991 0,973 0,166 0,187

Protein percentage

0,024 0,085 0,269 0,182 0,227 0,226 0,305 0,140

Estimated breeding values for bulls by different breeds

across joint population under breeding program of

Simmental cattle in Russia

LD decay between SNP in diapason from 100

kb to 10 Mb in Simmental origin and Holstein

cattle populations

Genome wide association study for milk production traits

EBV_Milk yield

EBV_Fat percentage

EBV_Protein percentage

Thank you for attention!

The research was carried out with the support and

assistance of:

Russian Foundation for Basic Research №17-44-500324

Ministry of Education and Science of Russian Federation

(№0445-2019-0027)