[1]
Safari A., Hossein-Zadeh N.G., Shadparvar A.A., Arpanahi R.A., A review on breeding
and genetic strategies in Iranian buffaloes (Bubalus bubalis), Tropical animal health
and production. 50 (2018) 707-714.
[2]
Iamartino D., Nicolazzi E.L., Van Tassell C.P., Reecy J.M., Fritz-Waters E.R., Koltes
J.E., Biffani S., Sonstegard T.S., Schroeder S.G., Ajmone-Marsan P., Design and validation
of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis), PloS one. 12
(2017) e0185220.
[3]
De Camargo G., Aspilcueta-Borquis R.R., Fortes M., Porto-Neto R., Cardoso D.F., Santos
D., Lehnert S., Reverter A., Moore S., Tonhati H., Prospecting major genes in dairy
buffaloes, BMC genomics. 16 (2015) 872.
[4]
Mokhber M., Moradi-Shahrbabak M., Sadeghi M., Moradi-Shahrbabak H., Stella A., Nicolzzi
E., Rahmaninia J., Williams J.L., A genome-wide scan for signatures of selection in
Azeri and Khuzestani buffalo breeds, BMC genomics. 19 (2018) 449.
[5]
Dhanda O., Developments in water buffalo in Asia and Oceania, in Proc. of the Seventh
World Buffalo Congress, Manila, Philippines, 2004, Vol. 20, pp. 17-28.
[6]
Howrigan D.P., Simonson M.A., Keller M.C., Detecting autozygosity through runs of
homozygosity: a comparison of three autozygosity detection algorithms, BMC genomics.
12 (2011) 460.
[7]
Broman K.W., Weber J.L., Long homozygous chromosomal segments in reference families
from the centre d'Etude du polymorphisme humain, The American Journal of Human Genetics.
65 (1999) 1493-1500.
[8]
Gibson J., Morton N.E., Collins A., Extended tracts of homozygosity in outbred human
populations, Human molecular genetics. 15 (2006) 789-795.
[9]
Peripolli E., Stafuzza N.B., Munari D.P., Lima A.L.F., Irgang R., Machado M.A., do
Carmo Panetto J.C., Ventura R.V., Baldi F., da Silva M.V.G.B., Assessment of runs
of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy
cattle, BMC genomics. 19 (2018) 34.
[10]
Zhang Q., Calus M.P., Guldbrandtsen B., Lund M.S., Sahana G., Estimation of inbreeding
using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds,
BMC genetics. 16 (2015) 88.
[11]
Marras G., Gaspa G., Sorbolini S., Dimauro C., Ajmone‐Marsan P., Valentini A., Williams
J.L., Macciotta N.P., Analysis of runs of homozygosity and their relationship with
inbreeding in five cattle breeds farmed in Italy, Animal genetics. 46 (2015) 110-121.
[12]
Purfield D.C., Berry D.P., McParland S., Bradley D.G., Runs of homozygosity and population
history in cattle, BMC genetics. 13 (2012) 70.
[13]
Kirin M., McQuillan R., Franklin C.S., Campbell H., McKeigue P.M., Wilson J.F., Genomic
runs of homozygosity record population history and consanguinity, PloS one. 5 (2010)
e13996.
[14]
Mastrangelo S., Tolone M., Di Gerlando R., Fontanesi L., Sardina M., Portolano B.,
Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity
in three local dairy cattle breeds, Animal. 10 (2016) 746-754.
[15]
Zhang Y., Young J., Wang C., Sun X., Wolc A., Dekkers J., Inbreeding by pedigree and
genomic markers in selection lines of pigs, in Proceedings of the 10th World Congress
of Genetics Applied to Livestock Production: WCGALP-2014, 2014.
[16]
Ghoreishifar S.M., Moradi-Shahrbabak H., Parna N., Davoudi P., Khansefid M., Linkage
disequilibrium and within-breed genetic diversity in Iranian Zandi sheep, Archives
Animal Breeding. 62 (2019) 143-151.
[17]
Mastrangelo S., Portolano B., Di Gerlando R., Ciampolini R., Tolone M., Sardina M.,
Consortium I.S.G., Genome-wide analysis in endangered populations: a case study in
Barbaresca sheep, Animal. 11 (2017) 1107-1116.
[18]
Purfield D.C., McParland S., Wall E., Berry D.P., The distribution of runs of homozygosity
and selection signatures in six commercial meat sheep breeds, PLoS One. 12 (2017)
e0176780.
[19]
Ghoreishifar S.M., Moradi-Shahrbabak H., Moradi-Shahrbabak M., Nicolazzi E.L., Williams
J.L., Iamartino D., Nejati-Javaremi A., Accuracy of imputation of single-nucleotide
polymorphism marker genotypes for water buffaloes (Bubalus bubalis) using different
reference population sizes and imputation tools, Livestock Science. 216 (2018) 174-182.
[20]
Williams J.L., Iamartino D., Pruitt K.D., Sonstegard T., Smith T.P., Low W.Y., Biagini
T., Bomba L., Capomaccio S., Castiglioni B., Genome assembly and transcriptome resource
for river buffalo, Bubalus bubalis (2 n= 50), GigaScience. 6 (2017) gix088.
[21]
Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D., Hanrahan F.,
Pertea G., Van Tassell C.P., Sonstegard T.S., A whole-genome assembly of the domestic
cow, Bos taurus, Genome biology. 10 (2009) R42.
[22]
Nicolazzi E.L., Iamartino D., Williams J.L., AffyPipe: an open-source pipeline for
Affymetrix Axiom genotyping workflow, Bioinformatics. 30 (2014) 3118-3119.
[23]
Chang C.C., Chow C.C., Tellier L.C., Vattikuti S., Purcell S.M., Lee J.J., Second-generation
PLINK: rising to the challenge of larger and richer datasets, GigaScience. 4 (2015).
[24]
Szmatoła T., Gurgul A., Ropka-Molik K., Jasielczuk I., Ząbek T., Bugno-Poniewierska
M., Characteristics of runs of homozygosity in selected cattle breeds maintained in
Poland, Livestock Science. 188 (2016) 72-80.
[25]
McQuillan R., Leutenegger A.-L., Abdel-Rahman R., Franklin C.S., Pericic M., Barac-Lauc
L., Smolej-Narancic N., Janicijevic B., Polasek O., Tenesa A., Runs of homozygosity
in European populations, The American Journal of Human Genetics. 83 (2008) 359-372.
[26]
Yang J., Lee S.H., Goddard M.E., Visscher P.M., GCTA: a tool for genome-wide complex
trait analysis, The American Journal of Human Genetics. 88 (2011) 76-82.
[27]
Huang D.W., Sherman B.T., Lempicki R.A., Bioinformatics enrichment tools: paths toward
the comprehensive functional analysis of large gene lists, Nucleic acids research.
37 (2008) 1-13.
[28]
Huang D.W., Sherman B.T., Lempicki R.A., Systematic and integrative analysis of large
gene lists using DAVID bioinformatics resources, Nature protocols. 4 (2008) 44.
[29]
Ferenčaković M., Sölkner J., Curik I., Estimating autozygosity from high-throughput
information: effects of SNP density and genotyping errors, Genetics Selection Evolution.
45 (2013) 42.
[30]
Bjelland D., Weigel K., Vukasinovic N., Nkrumah J., Evaluation of inbreeding depression
in Holstein cattle using whole-genome SNP markers and alternative measures of genomic
inbreeding, Journal of Dairy Science. 96 (2013) 4697-4706.
[31]
Pryce J.E., Haile-Mariam M., Goddard M.E., Hayes B.J., Identification of genomic regions
associated with inbreeding depression in Holstein and Jersey dairy cattle, Genetics
Selection Evolution. 46 (2014) 71.
[32]
Ghavi Hossein-Zadeh N., Analysis of population structure and genetic variability in
Iranian buffaloes (Bubalus bubalis) using pedigree information, Animal Production
Science. 56 (2016) 1130-1135.
[33]
Gaspa G., Marras G., Sorbolini S., Ajmone Marsan P., Williams J., Valentini A., Dimauro
C., Macciotta N., Genome-wide homozygosity in Italian Holstein cattle using HD panel,
in Proceedings of the 10th World Congress of Genetics Applied to Livestock Production,
2014, Vol. 17.
[34]
Zavarez L.B., Utsunomiya Y.T., Carmo A.S., Neves H.H., Carvalheiro R., Ferenčaković
M., Pérez O'Brien A.M., Curik I., Cole J.B., Van Tassell C.P., Assessment of autozygosity
in Nellore cows (Bos indicus) through high-density SNP genotypes, Frontiers in genetics.
6 (2015) 5.
[35]
Ferencakovic M., Hamzic E., Gredler B., Curik I., Sölkner J., Runs of homozygosity
reveal genome-wide autozygosity in the Austrian Fleckvieh cattle, Agriculturae Conspectus
Scientificus. 76 (2011) 325-329.
[36]
Kim E.-S., Cole J.B., Huson H., Wiggans G.R., Van Tassell C.P., Crooker B.A., Liu
G., Da Y., Sonstegard T.S., Effect of artificial selection on runs of homozygosity
in US Holstein cattle, PloS one. 8 (2013) e80813.
[37]
Rincon G., Farber E., Farber C., Nkrumah J., Medrano J., Polymorphisms in the STAT6
gene and their association with carcass traits in feedlot cattle, Animal genetics.
40 (2009) 878-882.
[38]
Nguyen L.T., Reverter A., Cánovas A., Venus B., Anderson S.T., Islas-Trejo A., Dias
M.M., Crawford N.F., Lehnert S.A., Medrano J.F., STAT6, PBX2, and PBRM1 emerge as
predicted regulators of 452 differentially expressed genes associated with puberty
in Brahman heifers, Frontiers in genetics. 9 (2018) 87.
[39]
Su R., Zhang W.-G., Sharma R., Chang Z.-L., Yin J., Li J.-Q., Characterization of
BMP 2 gene expression in embryonic and adult Inner Mongolia Cashmere goat (Capra hircus)
hair follicles, Canadian journal of animal science. 89 (2009) 457-462.
[40]
Fan B., Onteru S.K., Du Z.-Q., Garrick D.J., Stalder K.J., Rothschild M.F., Genome-wide
association study identifies loci for body composition and structural soundness traits
in pigs, PloS one. 6 (2011) e14726.
[41]
Lee J., Kang J.-H., Kim J.-M., Bayes Factor-Based Regulatory Gene Network Analysis
of Genome-Wide Association Study of Economic Traits in a Purebred Swine Population,
Genes. 10 (2019) 293.
[42]
Kim E.-S., Elbeltagy A., Aboul-Naga A., Rischkowsky B., Sayre B., Mwacharo J.M., Rothschild
M.F., Multiple genomic signatures of selection in goats and sheep indigenous to a
hot arid environment, Heredity. 116 (2016) 255.
[43]
Moioli B., Pilla F., Ciani E., Signatures of selection identify loci associated with
fat tail in sheep, Journal of Animal Science. 93 (2015) 4660-4669.
[44]
Yuan Z., Liu E., Liu Z., Kijas J., Zhu C., Hu S., Ma X., Zhang L., Du L., Wang H.,
Selection signature analysis reveals genes associated with tail type in Chinese indigenous
sheep, Animal genetics. 48 (2017) 55-66.
[45]
Nelson C.D., Reinhardt T.A., Beitz D.C., Lippolis J.D., In vivo activation of the
intracrine vitamin D pathway in innate immune cells and mammary tissue during a bacterial
infection, PloS one. 5 (2010) e15469.
[46]
Sharma G.T., Dubey P.K., Katiyar A., Kumar G.S., Localization and expression of proliferating
cell nuclear antigen (PCNA) and cyclin B1 in buffalo (Bubalus bubalis) ovary during
different stages of follicular development, Indian Journal of Animal Sciences. 81
(2011) 29-00.
[47]
Li C., Cai W., Zhou C., Yin H., Zhang Z., Loor J.J., Sun D., Zhang Q., Liu J., Zhang
S., RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration
in the Chinese Holstein population, Scientific reports. 6 (2016) 26813.
[48]
Carvalheira J., Salem M., Thompson G., Chen S., Beja-Pereira A., Genome-wide association
study for milk and protein yields in Portuguese Holstein cattle, MARS. 131 (2014)
131-183.
[49]
Araújo D.N., de Camargo G.M.F., Fonseca P.D.d.S., Cardoso D.F., Hurtado-Lugo N.A.,
Aspilcueta-Borquis R.R., Tonhati H., Polymorphisms in Oxytocin and α1a Adrenergic
Receptor Genes and Their Effects on Production Traits in Dairy Buffaloes, Animal biotechnology.
26 (2015) 165-168.
[50]
Fortes M., Reverter A., Kelly M., McCulloch R., Lehnert S., Genome‐wide association
study for inhibin, luteinizing hormone, insulin‐like growth factor 1, testicular size
and semen traits in bovine species, Andrology. 1 (2013) 644-650.
[51]
Abdoli R., Mirhoseini S.Z., Ghavi Hossein-Zadeh N., Zamani P., Ferdosi M.H., Gondro
C., Genome-wide association study of four composite reproductive traits in Iranian
fat-tailed sheep, Reprod Fertil Dev. (2019). https://doi.org/10.1071/RD18282
[52]
Cai Z., Guldbrandtsen B., Lund M.S., Sahana G., Dissecting closely linked association
signals in combination with the mammalian phenotype database can identify candidate
genes in dairy cattle, BMC genetics. 19 (2018) 30.
[53]
Xia J., Qi X., Wu Y., Zhu B., Xu L., Zhang L., Gao X., Chen Y., Li J., Gao H., Genome-wide
association study identifies loci and candidate genes for meat quality traits in Simmental
beef cattle, Mammalian genome. 27 (2016) 246-255.
[54]
Bai C., Pan Y., Wang D., Cai F., Yan S., Zhao Z., Sun B., Genome‐wide association
analysis of residual feed intake in Junmu No. 1 White pigs, Animal genetics. 48 (2017)
686-690.
[55]
Mészáros G., Petautschnig E., Schwarzenbacher H., Sölkner J., Genomic regions influencing
coat color saturation and facial markings in Fleckvieh cattle, Animal genetics. 46
(2015) 65-68.
[56]
Edea Z., Dadi H., Dessie T., Uzzaman M., Rothschild M., Kim E.S., Sonstegard T., Kim
K.S., Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations
from different regions, Animal genetics. 49 (2018) 550-563.
[57]
Urbinati I., Stafuzza N.B., Oliveira M.T., Chud T.C.S., Higa R.H., de Almeida Regitano
L.C., de Alencar M.M., Buzanskas M.E., Munari D.P., Selection signatures in Canchim
beef cattle, Journal of animal science and biotechnology. 7 (2016) 29.
[58]
Kühn C., Weikard R., An investigation into the genetic background of coat colour dilution
in a Charolais× German Holstein F2 resource population, Animal genetics. 38 (2007)
109-113.
[59]
Gutiérrez-Gil B., Wiener P., Williams J.L., Genetic effects on coat colour in cattle:
dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais× Holstein
population, BMC genetics. 8 (2007) 56.
[60]
Drögemüller C., Tetens J., Sigurdsson S., Gentile A., Testoni S., Lindblad-Toh K.,
Leeb T., Identification of the bovine Arachnomelia mutation by massively parallel
sequencing implicates sulfite oxidase (SUOX) in bone development, PLoS genetics. 6
(2010) e1001079.
[61]
Mastrangelo S., Sardina M., Tolone M., Di Gerlando R., Sutera A., Fontanesi L., Portolano
B., Genome-wide identification of runs of homozygosity islands and associated genes
in local dairy cattle breeds, animal. 12 (2018) 2480-2488.