北京黑猪HoxB簇基因多态性与脊椎数及胴体性状的关联分析

doi:10.11843/j.issn.0366-6964.2023.01.011

摘要/Abstract

摘要： 旨在对北京黑猪HoxB簇9个基因(HoxB1-7、9和13)的多态性与脊椎数和胴体性状(胴体长、胴体直长、胴体斜长及胴体重)进行关联分析。本研究提取251头220日龄的健康北京黑猪耳组织DNA，对HoxB簇的9个基因通过引物设计、聚合酶链式反应(PCR)技术、Sanger测序技术等对SNPs进行基因分型，并计算变异位点基因型频率以及等位基因频率分布，并与脊椎数和胴体性状进行关联分析。结果，本试验共筛选到4个基因共12个非编码区的(UTR)SNPs，包括HoxB2基因的1个5'UTR突变、HoxB5基因的2个3'UTR突变、HoxB9基因的2个3'UTR突变以及HoxB13基因的7个3'UTR突变。将12个SNPs分别与脊椎数和胴体性状使用Duncan's多重检验统计分析发现，HoxB2基因的1个5'UTR突变(c.40 C>T)、HoxB5基因的2个3'UTR突变(c.1766 A>G、c.1767 A>G)均与性状关联不显著(P>0.05)；而HoxB9基因中的1个3'UTR突变(c.2743 C>T)与胴体性状关联显著(P<0.05)，HoxB13基因中的2个3'UTR突变(c.1863 G>A、c.1440 A>C)与脊椎数关联显著(P<0.05)。综上所述，9个HoxB簇基因中仅HoxB9基因中1个3'UTR突变c.2743 C>T与胴体性状关联显著(P<0.05)，HoxB13基因2个3'UTR突变c.1863 G>A、c.1440 A>C均与脊椎数性状关联显著(P<0.05)，这3个位点可作为北京黑猪脊椎数及胴体性状变异的候选基因功能位点。

关键词: 北京黑猪, HoxB9, HoxB13, 脊椎数, 胴体性状

Abstract: The aim of this study was to investigate the association between polymorphisms of 9 genes (HoxB1-7,9 and 13) in HoxB cluster and vertebral number and carcass traits (carcass length, straight length, diagonal length and carcass weight) in Beijing black pigs. In this study, DNA was extracted from ear tissue of 251 healthy Beijing black pigs at the age of 220 days. The SNPs of 9 HoxB genes were genotyped by primer design, polymerase chain reaction (PCR) and Sanger sequencing, and the genotype frequency and allele frequency distribution of the mutated loci were calculated. The association analysis was performed between their polymorphism and the vertebral number and carcass traits. A total of 12 non-coding region (UTR) SNPs were detected in 4 genes, including one 5'UTR mutation of HoxB2, two 3'UTR mutation of HoxB5, two 3'UTR mutation of HoxB9 and seven 3'UTR mutation of HoxB13. Statistical analysis using Duncan’s multiple test revealed that a 5'UTR mutation of HoxB2 (c.40 C>T) and two 3'UTR mutations of HoxB5(c.1766 A>G and c.1767 A>G) associated with these traits indistinctively (P>0.05). A 3'UTR mutation of HoxB9 (c.2743 C>T) were significantly associated with carcass traits(P<0.05), and two 3'UTR mutations of HoxB13 (c.1863 G>A, c.1440 A>C) significantly associated with the vertebral number (P<0.05). In conclusion, among the 9 HoxB cluster genes, only one 3'UTR mutation (c.2743 C>T) in HoxB9 gene was significantly associated with carcass traits (P<0.05), two 3'UTR mutations (c.1863 G>A, c.1440 A>C) of HoxB13 gene were significantly associated with the vertebral number (P<0.05). Above the 3 SNPs could be used as candidate functional loci for the variation of vertebral number and carcass traits of Beijing black pigs.

Key words: Beijing black pigs, HoxB9, HoxB13, vertebral number, carcass traits

中图分类号:

S828.2

牛乃琪, 苏艳芳, 杨曼, 侯欣华, 王立刚, 张龙超. 北京黑猪HoxB簇基因多态性与脊椎数及胴体性状的关联分析[J]. 畜牧兽医学报, 2023, 54(1): 113-121.

NIU Naiqi, SU Yanfang, YANG Man, HOU Xinhua, WANG Ligang, ZHANG Longchao. Association Analysis of Polymorphisms of HoxB Cluster Genes with Vertebral Number and Carcass Traits in Beijing Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 113-121.

参考文献 43

[1]	SCAAL M.Early development of the vertebral column[J].Semin Cell Dev Biol,2016,49:83-91.
[2]	WELDON S A,MVNSTERBERG A E.Somite development and regionalisation of the vertebral axial skeleton[J].Semin Cell Dev Biol,2022,127:10-16.
[3]	WELDON S A,MVNSTERBERG A E.Somite development and regionalisation of the vertebral axial skeleton[J].Semin Cell Dev Biol,2022,127:10-16.
[4]	IIMURA T,DENANS N,POURQUIÉ O.Establishment of Hox vertebral identities in the embryonic spine precursors[J].Curr Top Dev Biol,2009,88:201-234.
[5]	NARITA Y,KURATANI S.Evolution of the vertebral formulae in mammals:a perspective on developmental constraints[J].J Exp Zool B Mol Dev Evol,2005,304(2):91-106.
[6]	KING J W B,ROBERTS R C.Carcass length in the bacon pig; its association with vertebrae numbers and prediction from radiographs of the young pig[J].Anim Prod,1960,2(1):59-65.
[7]	BURGOS C,LATORRE P,ALTARRIBA J,et al.Allelic frequencies of NR6A1 and VRTN,two genes that affect vertebrae number in diverse pig breeds:a study of the effects of the VRTN insertion on phenotypic traits of a Duroc×Landrace-Large White cross[J].Meat Sci,2015,100:150-155.
[8]	ANDERSON M J,MAGIDSON V,KAGEYAMA R,et al.Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function[J].Elife,2020,9:e55608.
[9]	OKUBO Y,SUGAWARA T,ABE-KODUKA N,et al.Lfng regulates the synchronized oscillation of the mouse segmentation clock via trans-repression of Notch signalling[J].Nat Commun,2012,3(1):1141.
[10]	BÖHMER C.Correlation between Hox code and vertebral morphology in the mouse:towards a universal model for Synapsida[J]. Zoological Lett,2017,3:8.
[11]	GODSAVE S,DEKKER E J,HOLLING T,et al.Expression patterns of Hoxb genes in the Xenopus embryo suggest roles in anteroposterior specification of the hindbrain and in dorsoventral patterning of the mesoderm[J].Dev Biol,1994,166(2):465-476.
[12]	李桃桃,金美林,费晓娟,等.Hox基因家族及其对动物脊椎形成的影响[J].畜牧兽医学报,2022,53(4):999-1009.LI T T,JIN M L,FEI X J,et al.The Hox gene family and its effects on spine formation in animals[J].Acta Veterinaria et Zootechnica Sinica,2022,53(4):999-1009.(in Chinese)
[13]	KRUMLAUF R.Hox genes,clusters and collinearity[J].Int J Dev Biol,2018,62(11-12):659-663.
[14]	DURSTON A J.Some questions and answers about the role of Hox temporal collinearity in vertebrate axial patterning[J].Front Cell Dev Biol,2019,7:257.
[15]	MALLO M,WELLIK D M,DESCHAMPS J.Hox genes and regional patterning of the vertebrate body plan[J].Dev Biol,2010,344(1):7-15.
[16]	GOUVEIA A,MARCELINO H M,GONÇALVES L,et al.Patterning in time and space:HoxB cluster gene expression in the developing chick embryo[J].Cell Cycle,2015,14(1):135-145.
[17]	NIU N,WANG H,SHI G,et al.Genome scanning reveals novel candidate genes for vertebral and teat number in the Beijing Black Pig[J].Anim Genet,2021,52(5):734-738.
[18]	ZHANG L C,WANG L G,LI Y,et al.A substitution within erythropoietin receptor gene D1 domain associated with litter size in Beijing Black pig,Sus scrofa[J].Anim Sci J,2011,82(5):627-632.
[19]	ERNST C W,STEIBEL J P.Molecular advances in QTL discovery and application in pig breeding[J].Trends Genet,2013, 29(4):215-224.
[20]	MIKAWA S,HAYASHI T,NII M,et al.Two quantitative trait loci on Sus scrofa chromosomes 1 and 7 affecting the number of vertebrae[J].J Anim Sci,2005,83(10):2247-2254.
[21]	FAN Y,XING Y Y,ZHANG Z Y,et al.A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and western pigs[J].PLoS One,2013,8(4):e62534.
[22]	QIAO R M,GAO J,ZHANG Z Y,et al.Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations[J].Genet Sel Evol,2015,47(1):17.
[23]	GUO Y M,HUANG Y X,HOU L J,et al.Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches[J].Genet Sel Evol,2017,49(1):21.
[24]	LI L Y,XIAO S J,TU J M,et al.A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations[J].Anim Genet,2021,52(5):621-632.
[25]	DESCHAMPS J,VAN NES J.Developmental regulation of the Hox genes during axial morphogenesis in the mouse[J].Development,2005,132(13):2931-2942.
[26]	MEDINA-MARTÍNEZ O,BRADLEY A,RAMÍREZ-SOLIS R.A large targeted deletion of Hoxb1-Hoxb9 produces a series single-segment anterior homeotic transformations[J].Dev Biol,2000,222(1):71-83.
[27]	GOH K L,YANG J T,HYNES R O.Mesodermal defects and cranial neural crest apoptosis in alpha5 integrin-null embryos[J]. Development,1997,124(21):4309-4319.
[28]	CHEN F,CAPECCHI M R.Targeted mutations in Hoxa-9 and Hoxb-9 reveal synergistic interactions[J].Dev Biol,1997,181(2):186-196.
[29]	MCINTYRE D C,RAKSHIT S,YALLOWITZ A R,et al.Hox patterning of the vertebrate rib cage[J].Development, 2007, 134(16):2981-2989.
[30]	XU B,WELLIK D M.Axial Hox9 activity establishes the posterior field in the developing forelimb[J].Proc Natl Acad Sci U S A,2011,108(12):4888-4891.
[31]	AIRES R,DE LEMOS L,NÓVOA A,et al.Tail bud progenitor activity relies on a network comprising Gdf11,Lin28,and Hox13 genes[J].Dev Cell,2019,48(3):383-395.e8.
[32]	AMIN S,NEIJTS R,SIMMINI S,et al.Cdx and T brachyury Co-activate growth signaling in the embryonic axial progenitor niche[J].Cell Rep,2016,17(12):3165-3177.
[33]	MALLO M.Reassessing the role of Hox genes during vertebrate development and evolution[J].Trends Genet,2018,34(3):209-217.
[34]	STEVENTON B,MARTINEZ ARIAS A.Evo-engineering and the cellular and molecular origins of the vertebrate spinal cord[J].Dev Biol,2017,432(1):3-13.
[35]	ECONOMIDES K D,ZELTSER L,CAPECCHI M R.Hoxb13 mutations cause overgrowth of caudal spinal cordand tail vertebrae[J].Dev Biol,2003,256(2):317-330.
[36]	LAPPIN T R J,GRIER D G,THOMPSON A,et al.HOX GENES:seductive science,mysterious mechanisms[J].Ulster Med J,2006, 75(1):23-31.
[37]	WELLIK D M.Hox genes and kidney development[J].Pediatr Nephrol,2011,26(9):1559-1565.
[38]	XIE X H,LU J,KULBOKAS E J,et al.Systematic discovery of regulatory motifs in human promoters and 3'UTRs by comparison of several mammals[J].Nature,2005,434(7031):338-345.
[39]	BERKOVITS B D,MAYR C.Alternative 3'UTRs act as scaffolds to regulate membrane protein localization[J].Nature, 2015, 522(7556):363-367.
[40]	MAYR C.What are 3' UTRs doing?[J].Cold Spring Harb Perspect Biol,2019,11(10):a034728.
[41]	YAMAGUCHI T,KAWAGUCHI A,KIM Y I,et al.The role of polymorphisms associated with early tooth eruption in dental and occlusal traits in East Asian populations[J].Korean J Orthod,2014,44(2):96-102.
[42]	SAUNDERS E J,DADAEV T,LEONGAMORNLERT D A,et al.Fine-mapping the HOXB region detects common variants tagging a rare coding allele:evidence for synthetic association in prostate cancer[J].PLoS Genet,2014,10(2):e1004129.
[43]	CLEMENCEAU A,BOUCHERAT O,LANDRY-TRUCHON K,et al.Lung cancer susceptibility genetic variants modulate HOXB2 expression in the lung[J].Int J Dev Biol,2018,62(11-12):857-864.