Identification of Markers Associated with Birth Weight in Boer Goat

Saadiah Jamli


Genetic improvement of breeding depends on selective breeding of superior phenotypes. In order to increase accuracy of breeding and selection for efficient production systems, current trend is towards applying molecular markers. The purpose of the study was to identify markers associated with birth weight in Boer goats using 50k single nucleotide polymorphism (SNP) chip. A total of 657 Boer goats were selected based on the availability of birth weight data from a commercial farm. Individuals were genotyped using 50k SNP chip from Illumina using Illumina Genome Analyzer IIx. A genome wide association analysis using a mixed model was carried out and resulted in 32 detected markers for birth weight. In previous genotyping study done on the same population of goat using 20k custom-designed SNP chip resulted in 14 markers for birth weight. However, markers identified should be verified in an independent population before being applied in a Marker Assisted Selection (MAS) program. Further consideration should be on socio-economic factors as well as their sustainability in biodiverse environments.


Molecular Markers; 50k SNP Chip; Boer Goat


Aulchenko YS, De Koning DJ, Haley C. 2007. Genome wide rapid association using mixed model and regression: A fast and simple method for genome wide pedigree-based quantitative trait loci association analysis. Genetics. 177:577-585.

Brito LF, Jafarikia M, Grossi DA, Kijas JW, Porto-Neto LR, Ventura RV, Salgorzaei M, Chenkel FS. 2015. Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats. BMC Genetics. DOI: 10.1186/s12863-015-0220-1.

Dekkers JCM. 2004. Commercial application of marker- and gene-assisted selection in livestock: Strategies and lessons. J Anim Sci. 82(E Suppl.):E313-E328.

Esmailizadeh AK. 2014. Genome-scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus) Anim Genet. 45:849-854.

Farah MM, Swan AA, Fortes MRS, Fonseca R, Moore SS, Kelly MJ. 2016. Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle. Anim Genet. 47:3-11.

Greenwood PL, Hunt AS, Hermanson JW, Bell AW. 1998. Effects of birth weight and postnatal nutrition on neonatal sheep: I. Body growth and composition, and some aspects of energetic efficiency. J Anim Sci. 76:2354-2367.

Groeneveld LF, Lenstra J, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S, The GLOBALDIV Consortium. 2010. Genetic diversity in farm animals-a review. Anim Genet. 41 (Suppl. 1):6-31.

Jung EJ, Park HB, Lee JB, Yoo CK, Kim BM, Kim HI, Kim BW, Lim HT. 2014. Genome-wide association analysis identifies quantitative trait loci for growth in a Landrace purebred population. Anim Genet. 45:442-444.

Leroy G. 2014. Inbreeding depression in livestock species: review and meta-analysis. Anim Genet. 45:618-628.

Manunza A, Noce A, Serradilla JM, Goyache F, Martínez A, Capote J, Delgado JV, Jordana J, Muñoz E, Molina A, Landi V, Pons A, Balteanu V, Traoré A, Vidilla M, Rodriguez MS, Sànchez A, Cardoso TF, Amills M. 2016. A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds. Genet Sel Evol. 48:52.

Morel PCH, Morris ST, Kenyon PR. 2008. Effect of birth weight on survival in triplet-born lambs. Aust J Exp Agric. 48:984-987.

Nicoloso L, Bomba L, Colli L, Negrini R, Milanesi M, Mazza R, Sechi T, Frattini S, Talenti A, Coizet B, Chessa S, Marletta D, D’Andrea M, Bordonaro S, Ptak G, Carta A, Pagnacco G, Valentini A, Pilla F, Ajmone-Marsan P, Crepaldi P. 2015. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip. The Italian Goat Consortium. Genet Select Evol. 47:62.

Montaldo HH, Meza-Herrera CA. 1998. Use of molecular markers and major genes in the genetic improvement of livestock. J Biotechnol. 1:1-9.

Onogi A, Ogino A, Komatsu T, Shoji N, Shimizu K, Kurogi K, Yasumori T, Togashi K, Iwata H. 2015. Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle. Anim Genet. 46:557-559.

Ortega MS, Denicol AC, Cole JB, Null DJ, Hansen PJ. 2016. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for rediction of genetic merit for reproduction in Holstein cows. Anim Genet. 47:288-297.

Saadiah J, Johari JA, Tun-Ping Y, Nadaf J, Hifzan RM, Ernie-Muneerah MA, Khairun Hisam N, Rabiatul-Adawiyah ZA, Umi-Kalsom AB. 2014. A genome wide association study for birth weight in boer goats using a 20k single nucleotide polymorphism chip. MJVR. 5:305-307.

Sasaki S, Ibi T, Kojima T, Sugimoto Y. 2015. A genome-wide association study reveals a quantitative trait locus for days open on chromosome 2 in Japanese Black Cattle. Anim Genet. 47:102-105.

Skok DJ, Kunej T, Kovac M, Malovrh S, Potocnik K, Petric N, Zgur S, Dovc P, Horvat S. 2016. FTO gene variants are associated with growth and carcass traits in cattle. Anim Genet. 47:219-222.

Somavilla AL, Sonstegard TS, Higa RH, Rosa AN, Siqueira F, Silva LOC, Torres Junior RAA, Coutinho LL, Mudadu MA, Alencar MM, Regitano LCA. 2014. A genome-wide scan for selection signatures in Nellore cattle. Anim Genet. 45:771-781.

Tart JK, Johnson RK, Bundy JW, Ferdinand NN, McKnite AM, Wood JR, Miller PS, Rothschild MF, Spangler ML, Garrick DJ, Kachman SD, Ciobanu DC. 2013. Genome-wide prediction of age at puberty and reproductive longevity in sows. Anim Genet. 44:387-397.

Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieu-Tonon C, Eggen A, Heuven HCM, Jamli S, Jiken AJ, Klopp C, Lawley CT, McEwan J, Martin P, Moreno CR, Mulsant P, Nabihoudine I, Pailhoux E, Palhie`re I, Rupp R, Sarry J, Sayre BL, Tircazes A, Wang J, Wang W, Zhang W. 2014. Design and Characterization of a 52K SNP Chip for Goats. The International Goat Genome Consortium. PLoS One. 9:e86227.

Visser C, Lashmar SF, Marle-Köster EV, Poli MA, Allain D. 2016. Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP Data. PLoS One 11:e0154353. doi: 10.1371/journal.pone.0154353.

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DOI: 10.14334/Proc.Intsem.LPVT-2016-p.247-251


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