Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

被引：84

作者：

Munoz, M. ^{[1
]}

Bozzi, R. ^{[2
]}

Garcia-Casco, J. ^{[1
]}

Nunez, Y. ^{[1
]}

Ribani, A. ^{[3
]}

Franci, O. ^{[2
]}

Garcia, F. ^{[1
]}

Skrlep, M. ^{[4
]}

Schiavo, G. ^{[3
]}

Bovo, S. ^{[3
]}

Utzeri, V. J. ^{[3
]}

Charneca, R. ^{[5
]}

Martins, J. M. ^{[5
]}

Quintanilla, R. ^{[6
]}

Tibau, J. ^{[6
]}

Margeta, V. ^{[7
]}

Djurkin-Kusec, I. ^{[7
]}

Mercat, M. J. ^{[8
]}

Riquet, J. ^{[9
]}

Estelle, J. ^{[10
]}

Zimmer, C. ^{[11
]}

Razmaite, V. ^{[12
]}

Araujo, J. P. ^{[13
]}

Radovic, C. ^{[14
]}

Savic, R. ^{[15
]}

Karolyi, D. ^{[16
]}

Gallo, M. ^{[17
]}

Candek-Potokar, M. ^{[4
]}

Fernandez, A. I. ^{[1
]}

Fontanesi, L. ^{[3
]}

Ovilo, C. ^{[1
]}

机构：

[1] INIA, Dept Mejora Genet Anim, Madrid, Spain

[2] Univ Firenze, DAGRI, Anim Sci Sect, Florence, Italy

[3] Univ Bologna, Dept Agr & Food Sci, Bologna, Italy

[4] Agr Inst Slovenia, Hacquetova Ulica 17, SI-1000 Ljubljana, Slovenia

[5] Univ Evora, ICAAM, Evora, Portugal

[6] IRTA, Programa Genet & Mejora Anim, Barcelona, Spain

[7] Univ Osijek, Fac Agrobiotech Sci Osijek, Osijek, Croatia

[8] IFIP Inst Porc, Le Rheu, France

[9] INRA, Genet Physiol & Syst Elevage, Castanet Tolosan, France

[10] Univ Paris Saclay, AgroParisTech, INRA, GABI, Jouy En Josas, France

[11] Bauerliche Erzeugergemeinschaft Schwabisch Hall, Wolpertshausen, Germany

[12] Lithuanian Univ Hlth Sci, Anim Sci Inst, Baisogala, Lithuania

[13] Escola Super Agr, Inst Politecn Viana Castelo, Ctr Invest Montanha CIMO, Ponte do Lima, Portugal

[14] Inst Anim Husb, Pig Res Dept, Autoput Zagreb 16, Belgrade 11080, Serbia

[15] Univ Belgrade, Fac Agr, Nemanjina 6, Belgrade 11080, Serbia

[16] Univ Zagreb, Dept Anim Sci, Fac Agr, Zagreb, Croatia

[17] ANAS, Rome, Italy

来源：

SCIENTIFIC REPORTS | 2019年 / 9卷 / 1期

关键词：

EFFECTIVE POPULATION-SIZE; GENETIC DIVERSITY; IDENTIFICATION; POLYMORPHISM; ASSOCIATION; EVOLUTION; FATNESS; GROWTH; DNA;

D O I：

10.1038/s41598-019-49830-6

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

引用

页数：14

共 81 条

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