基于RAD-seq简化基因组测序的19个地方鸡种遗传进化研究

doi:10.11843/j.issn.0366-6964.2020.04.003

Abstract

Abstract: The purposes of this study were to reveal the genetic evolution of local chicken breeds at the genomic level and to discover genes with important germplasm characteristics. Restriction site-associated DNA sequencing (RAD-seq) technology was employed to identify single nucleotide polymorphism (SNP) markers in 19 indigenous chicken breeds. For each breed, thirty individuals(10 males and 20 females) were selected as experimental materials according to their family records. The genetic diversity and structure were analyzed by calculating the indicators of genetic statistics, which contained observed heterozygosity (Ho), nucleotide diversity (Pi), inbreeding coefficients (Fis), genetic differentiation coefficients (Fst) and gene flows (Nm). The selected genes were also identified through genome selective signals testing. The results showed that 400 562 SNP markers were identified in 19 indigenous chicken populations after data quality control. The PJ and WC populations had the highest genetic diversity, with Ho 0.246 8, 0.243 0, and Pi 0.278 1, 0.265 5, respectively. The DJ population had the lowest Ho and Pi, which were 0.156 0 and 0.157 2,respectively. The Fis in DX and BJ populations were higher than 0.160 0. The Fst among PJ and WC, HX, ZZ, WX, HX and WC, ZZ and CH were all lower than 0.100 0, correspondingly the Nm were all higher than 0.240 0. In terms of single population, the DJ population had higher Fst and lower Nm when compared to other chicken breeds. The phylogenetic tree, constructed using two foreign chicken breeds AK and RW as outgroups, divided the 19 indigenous chicken breeds into 5 clusters, which was consistent with their breeding history and geography distribution. In total, 26 selected areas and 31 candidate genes were identified through the Z transformation of heterozygosity (ZHp) signal testing. These selected genes were widely involved in the biological processes of immune system regulation, reproduction regulation, response to stress and metabolism. In conclusion, the genomic SNP markers have more advantage in revealing genetic diversity and structure of indigenous chicken breeds. The selection effects are mainly reflected in the shaping of local chicken breeds' resistance and disease resistance characteristics, gamete vitality and behavior.

Key words: indigenous chicken breed, RAD-seq, genetic evolution, selective signal

CLC Number:

S831.2

HAN Wei, ZHU Yunfen, YIN Jianmei, LI Guohui, XUE Qian, ZHANG Huiyong, SHEN Haiyu, SU Yijun, DOU Xinhong, WANG Kehua, ZOU Jianmin. Study on Genetic Evolution of 19 Indigenous Chicken Breeds Based on RAD-seq[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(4): 670-678.

References 40

[1]	QU L J,LI X Y,XU G F,et al.Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers[J].Science in China Series C Life Sciences,2006,49(4):332-341.
[2]	高玉时,唐修君,屠云洁,等.基于线粒体COⅠ基因15个鸡种的DNA编码研究[J].中国农业科学,2011,44(3):587-594.GAO Y S,TANG X J,TU Y J,et al.Studies on the DNA barcoding of fifteen chicken breeds by mtDNA COⅠ gene[J].Scientia Agricultura Sinica,2011,44(3):587-594.(in Chinese)
[3]	DAVEY J W,HOHENLOHE P A,ETTER P D,et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nat Rev Genet,2011,12(7):499-510.
[4]	HOHENLOHE P A,BASSHAM S,ETTER P D,et al.Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags[J].PLoS Genet,2010,6(2):e1000862.
[5]	EMERSON K J,MERZ C R,CATCHEN J M,et al.Resolving postglacial phylogeography using high-throughput sequencing[J].Proc Natl Acad Sci U S A,2010,107(37):16196-16200.
[6]	HOHENLOHE P A,AMISH S J,CATCHEN J M,et al.Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout[J].Mol Ecol Resour,2011,11(S1):117-122.
[7]	RUBIN C J,ZODY M C,ERIKSSON J,et al.Whole-genome resequencing reveals loci under selection during chicken domestication[J].Nature,2010,464(7288):587-592.
[8]	贡潘偏抽,刘丽仙,李大林,等.基于线粒体DNA控制区(mtDNA D-loop)序列分析瓢鸡的遗传多样[J].云南农业大学学报,2011,26(2):211-214,223.GONGPAN P C,LIU L X,LI D L,et al.The investigation of genetic diversity of Piao Chicken based on mitochondrial DNA D-loop region sequence[J].Journal of Yunnan Agricultural University,2011,26(2):211-214,223.(in Chinese)
[9]	顾玉兰,刘小林,张建勤.文昌鸡群体内遗传变异分析[J].西北农业学报,2008,17(4):28-31.GU Y L,LIU X L,ZHANG J Q.Genetic variation in Wenchang chicken[J].Acta Agriculturae Boreali-Occidentalis Sinica, 2008, 17(4):28-31.(in Chinese)
[10]	陈宽维,李慧芳,王金玉,等.华东27个地方鸡品种(品系)的遗传变异[J].畜牧兽医学报,2006,37(1):7-11.CHEN K W,LI H F,WANG J Y,et al.Study on genetic diversity of 27 indigenous chicken breeds or strains in East China[J]. Acta Veterinaria et Zootechnica Sinica,2006,37(1):7-11.(in Chinese)
[11]	SABETI P C,VARILLY P,FRY B,et al.Genome-wide detection and characterization of positive selection in human populations[J]. Nature,2007,449(7164):913-918.
[12]	HUERTA-SÁNCHEZ E,JIN X,ASAN,et al.Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA[J]. Nature,2014,512:194-197.
[13]	LI M Z,TIAN S L,JIN L,et al.Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars[J].Nat Genet,2013,45(12):1431-1438.
[14]	YANG S B,LI X L,LI K,et al.A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds[J].BMC Genet,2014,15(1):7.
[15]	WEI C H,WANG H H,LIU G,et al.Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds[J].BMC Genomics,2015,16(1):194.
[16]	ELFERINK M G,MEGENS H J,VEREIJKEN A,et al.Signatures of selection in the genomes of commercial and non-commercial chicken breeds[J].PLoS One,2012,7(2):e32720.doi:10.1371/journal.pone.0032720.
[17]	WANG M S,LI Y,PENG M S,et al.Genomic analyses reveal potential independent adaptation to high altitude in Tibetan Chickens[J].Mol Biol Evol,2015,32(7):1880-1889.
[18]	WANG M S,ZHANG R W,SU L Y,et al.Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication[J].Cell Res,2016,26(5):556-573.
[19]	LI L,FENG W G,CHENG Z Q,et al.TRIM62-mediated restriction of avian leukosis virus subgroup J replication is dependent on the SPRY domain[J].Poult Sci,2019,98(11):6019-6025.
[20]	ZHANG S,TAKAKU M,ZOU L Y,et al.Reversing SKI-SMAD4-mediated suppression is essential for TH17 cell differentiation[J].Nature,2017,551(7678):105-109.
[21]	O'CONNELL P A,SURETTE A P,LIWSKI R S,et al.S100A10 regulates plasminogen-dependent macrophage invasion[J]. Blood,2010,116(7):1136-1146.
[22]	ZHANG H B,HOU Y J,HAN S Y,et al.Mammalian nitrilase 1 homologue Nit1 is a negative regulator in T cells[J].Int Immunol,2009,21(6):691-703.
[23]	LIU Z L,OYOLA M G,ZHOU S L,et al.Knockout of the histone demethylase Kdm3b decreases spermatogenesis and impairs male sexual behaviors[J].Int J Biol Sci,2015,11(12):1447-1457.
[24]	LIU Z L,CHEN X,ZHOU S L,et al.The histone H3K9 demethylase Kdm3b is required for somatic growth and female reproductive function[J].Int J Biol Sci,2015,11(5):494-507.
[25]	SAXE J P,CHEN M J,ZHAO H Y,et al.Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline[J].EMBO J,2013,32(13):1869-1885.
[26]	SUN F Y,PALMER K,HANDEL M A.Mutation of Eif4g3,encoding a eukaryotic translation initiation factor,causes male infertility and meiotic arrest of mouse spermatocytes[J].Development,2010,137(10):1699-1707.
[27]	MAGEE J A,CHANG L W,STORMO G D,et al.Direct,androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element[J].Endocrinology,2006,147(1):590-598.
[28]	SUN Y J,ZHANG P,ZHENG H,et al.Chicken RNA-binding protein T-cell internal antigen-1 contributes to stress granule formation in chicken cells and tissues[J].J Vet Sci,2018,19(1):3-12.
[29]	UCKELMANN M,DENSHAM R M,BAAS R,et al.USP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A[J].Nat Commun,2018,9(1):229.
[30]	VELIMEZI G,ROBINSON-GARCIA L,MUÍOZ-MARTÍNEZ F,et al.Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48[J].Nat Commun,2018,9(1):2280.
[31]	WANG Y D,ZHANG J,LI C H,et al.Molecular cloning,sequence characteristics,and tissue expression analysis of ECE1 gene in Tibetan pig[J].Gene,2015,571(2):237-244.
[32]	KHAMAISI M,TOUKAN H,AXELROD J H,et al.Endothelin-converting enzyme is a plausible target gene for hypoxia-inducible factor[J].Kidney Int,2015,87(4):761-770.
[33]	FIGEAC N,MOHAMED A D,SUN C S,et al.VGLL3 operates via TEAD1,TEAD3 and TEAD4 to influence myogenesis in skeletal muscle[J].J Cell Sci,2019,132(13):jcs225946.
[34]	JOSHI S,DAVIDSON G,LE GRAS S,et al.TEAD transcription factors are required for normal primary myoblast differentiation in vitro and muscle regeneration in vivo[J].PLoS Genet,2017,13(2):e1006600
[35]	VANONI M A.Structure-function studies of MICAL,the unusual multidomain flavoenzyme involved in actin cytoskeleton dynamics[J].Arch Biochem Biophys,2017,632:118-141.
[36]	FRÉMONT S,ROMET-LEMONNE G,HOUDUSSE A,et al.Emerging roles of MICAL family proteins-from actin oxidation to membrane trafficking during cytokinesis[J].J Cell Sci,2017,130(9):1509-1517.
[37]	HERRERA-MARCOS L V,LOU-BONAFONTE J M,MARTINEZ-GRACIA M V,et al.Prenylcysteine oxidase 1,a pro-oxidant enzyme of low density lipoproteins[J].Front Biosci (Landmark Ed),2018,23:1020-1037.
[38]	WATSCHINGER K,WERNER E R.Alkylglycerol monooxygenase[J].IUBMB Life,2013,65(4):366-372.
[39]	LIN J C.Multi-posttranscriptional regulations lessen the repressive effect of SRPK1 on brown adipogenesis[J].Biochim Biophys Acta:Mol Cell Biol Lipids,2018,1863(5):503-514.
[40]	LIAQAT K,CHIU I,LEE K,et al.Novel missense and 3'-UTR splice site variants in LHFPL5 cause autosomal recessive nonsyndromic hearing impairment[J].J Hum Genet,2018,63(11):1099-1107.

Study on Genetic Evolution of 19 Indigenous Chicken Breeds Based on RAD-seq

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