|
|
|
| Whole-genome Resequencing Reveals Variant Associated with Polled Traits in Mongolia Cattle (Bos Taurus) |
| GU Ming-Juan, LUO Rong-Song, GAO Li, ZHOU Xin-Yu, WU Di WEI, Zhu-Ying, BAI Chun-Ling, WU Yun-Xi, LI Guang-Peng* |
| State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock,Inner Mongolia University,Hohhot 010070,China |
|
|
|
|
Abstract The absence of horns or polled phenotype is desirable in the modern cattle industry for their beneficial to animal welfare and reduction of breeding costs. In this study,Illumina-based whole-genome resequencing of seven Mongolia cattle (Bos Taurus) (3 horn,4 polled) was reported. The whole genomic DNA was used to prepare 350 bp pair-end libraries and the high-throughput sequencing yielded 380.88 Gb. Comparative genomic analyses identified 11 362 382 genome-wide single nucleotide polymorphisms (SNPs) and 1 150 664 insertions/deletions (InDels),Most of the variations (96% of SNPs and 94% of InDels) were located in intergenic,transcript and intron regions,noted 3 768 genes. After screening,20 differential genes were related to the horn growth and development. Meanwhile,the population stratification analysis of SNPs and InDels showed that hornless traits did not cause genetic differentiation of Mongolian cattle. Further analysis by sequence,polymerase chain reaction (PCR),agarose gel electrophoresis and Sanger sequencing showed that the Mongolia cattle POLLED genotype belongs to P219ID mutation. This study provides baseline data for further research to investigate the molecular mechanisms of polled trait,and provides a valuable resource for genetic characteristics of Mongolia cattle.
|
|
Received: 16 January 2020
|
|
|
|
Corresponding Authors:
*gpengli@imu.edu.cn
|
|
|
|
[1] 陈幼春,曹红鹤.2001.中国黄牛品种多样性及其保护[J].生物多样性,9(3):275-283.
(Chen Y C,Cao H H.2001.Diversity of Chinese yellow cattle breeds and their conservation[J].Biodiversity Science,9(3):275-283.)
[2] 齐昱.2017.基于转录组学的蒙古牛抗寒机制的研究[D].博士学位论文,内蒙古农业大学,导师:周欢敏,pp.1.
(Qi Y.2017.Study on cold resistance mechanism of Mongolian Cattle based on transcriptome[D].Thesis for M.S.,Inner Mongolia Agricultural University,Supervisor:Zhou H M,pp.1.)
[3] Allais-Bonnet A,Grohs C,Medugorac I,et al.2013.Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae[J].Plos One,8(5):e63512.
[4] Carlson D F,Lancto C A,Zang B,et al.2016.Production of hornless dairy cattle from genome-edited cell lines[J].Nature Biotechnology,34(5):479-481.
[5] Chen S Y,Liu L H,Fu M Z,et al.2017.Simultaneous introgression of three POLLED mutations into a synthetic breed of Chinese cattle[J].Plos One,12(10):e0186862.
[6] Choi J W,Liao X,Park S,et al.2013.Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels[J].Molecules and Cells,36(3):203‐211.
[7] Elsik C G,Tellam R L,Worley K C,et al.2009.The genome sequence of taurine cattle:A window to ruminant biology and evolution[J].Science,324(5926):522‐528.
[8] Frazer K A,Eskin E,Kang H M,et al.2007.A sequence-based variation map of 8.27 million SNPs in inbred mouse strains[J].Nature,448(7157):1050‐1053.
[9] Gilissen C,Hoischen A,Brunner H G,et al.2012.Disease gene identification strategies for exome sequencing[J].European Journal of Human Genetics,20(5):490‐497.
[10] Iqbal N,Liu X,Yang T,et al.2019.Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan[J].Plos One,14(4):e0215065.
[11] Jiang A,Zhang J,Yuan C B,et al.2019.Whole-genome scanning for the heat-resistance-associated genes in the Droughtmaster breed (Bos taurus)[J].3 Biotech,9(3):95-104.
[12] Kawahara-Miki R,Tsuda K,Shiwa Y,et al.2011.Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi[J].BMC Genomics,12:103.
[13] Kim J,Hanotte O,Mwai O A,et al.2017.The genome landscape of indigenous African cattle[J].Genome Biology,18(1):34.
[14] Koboldt D C,Steinberg K M,Larson D E,et al.2013.The next-generation sequencing revolution and its impact on genomics[J].Cell,155(1):27‐38.
[15] Ku C S,Naidoo N,Pawitan Y.2011.Revisiting mendelian disorders through exome sequencing[J].Human Genetics,129(4):351‐370.
[16] Laine J M,Todd F D,Suzanne T M,et al.2007.An investigation into the practices of dairy producers and veterinarians in dehorning dairy calves in Ontario[J].The Canadian Veterinary Journal,48(12):1249-1254.
[17] Larkin D M,Daetwyler H D,Hernandez A G,et al.2012.Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle[J].Proceedings of the National Academy of Sciences of the USA,109(20):7693-7698.
[18] Liang C N,Wang L Z,Wu X Y,et al.2016.Genome-wide association study identifies loci for the polled phenotype in yak[J].Plos One,11(7):e0158642.
[19] Lin S,Zhang H Y,Hou Y L,et al.2019.SNV discovery and functional candidate gene identification for milk composition based on whole genome resequencing of Holstein bulls with extremely high and low breeding values[J].Plos One,14(8):e0220629.
[20] Liu W B,Liu J,Liang C N,et al.2014.Associations of single nucleotide polymorphisms in candidate genes with the polled trait in Datong domestic yaks[J].Animal Genetics,45(1):138-141.
[21] Matthew L S,Sarah L B,Dee G,et al.2013.Bovine Dehorning[J].Veterinary Clinics of North America:Food Animal Practice,29(1):103-133.
[22] Medugorac I,Graf A,Grohs C,et al.2017.Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks[J].Nature Genetics,49(3):470-475.
[23] Medugorac I,Seichter D,Graf A,et al.2012.Bovine polledness-an autosomal dominant trait with allelic heterogeneity[J].Plos One,7(6):e39477.
[24] Metzker M L.2010.Sequencing technologies-the next generation[J].Nature Reviews,11(1):31‐46.
[25] Prayaga K C.2007.Genetic options to replace dehorning in beef cattle-a review[J].Australian Journal of Agricultural Research,58(1):1-8.
[26] Qiu Q,Wang L Z,Wang K,et al.2015.Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions[J].Nature Communications,6(1):10283.
[27] Rothammer S,Capitan A,Mullaart E,et al.2014.The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype of Friesian origin[J].Genetics Selection Evolution,46(1):44-48.
[28] Schmutz S M,Marquess F L,Berryere T G,et al.1995.DNA marker-assisted selection of the polled condition in Charolais cattle[J].Mammalian genome:Official journal of the International Mammalian Genome Society,6(10):710-713.
[29] Spillman W J.1906.Mendel's law in relation to animal breeding[J].Journal of Heredity,1(2):171-177.
[30] Stafford K J,Mellor D J.2005.Dehorning and disbudding distress and its alleviation in calves[J].The Veterinary Journal,169(3):337-349.
[31] Tellam R L,Lemay D G,Van Tassell C P,et al.2009.Unlocking the bovine genome[J].BMC Genomics,10:193.
[32] Utsunomiya Y T,Torrecilha R B P,Milanesi M,et al.2019.Hornless Nellore cattle (Bos indicus) carrying a novel 110 kbp duplication variant of the polled locus[J].Animal Genetics,50(2):187-188.
[33] Wiedemar N,Tetens J,Jagannathan V,et al.2014.Independent polled mutations leading to complex gene expression differences in cattle[J].Plos One,9(3):e93435.
[34] Wiener D J,Wiedemar N,Welle M M,et al.2015.Novel features of the prenatal horn bud development in cattle (Bos taurus)[J].Plos One,10(5):e0127691.
[35] Zhang F W,Qu K X,Chen N B,et al.2019.Genome-wide SNPs and InDels characteristics of three Chinese cattle breeds[J].Animals,9(9):596-605. |
|
|
|
