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Yuan Y, Zhang H, Yi G, You Z, Zhao C, Yuan H, Wang K, Li J, Yang N, Lian L. Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations. Front Genet 2021; 12:710770. [PMID: 34484301 PMCID: PMC8414643 DOI: 10.3389/fgene.2021.710770] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.
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Affiliation(s)
- Yiming Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanmin Zhang
- United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhen You
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunfang Zhao
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haixu Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Haunshi S, Devara D, Ramasamy K, Ullengala R, Chatterjee RN. Genetic diversity at major histocompatibility complex and its effect on production and immune traits in indigenous chicken breeds of India. Arch Anim Breed 2020; 63:173-182. [PMID: 32760784 PMCID: PMC7397721 DOI: 10.5194/aab-63-173-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/12/2020] [Indexed: 12/03/2022] Open
Abstract
The genetic diversity at major histocompatibility complex (MHC) in indigenous chicken breeds of India
(Ghagus and Nicobari) in comparison with the White Leghorn (WLH) breed was
investigated by genotyping the MHC-linked LEI0258 marker. Altogether 38 alleles
and 96 genotypes were observed among three breeds. The observed and
effective alleles were highest in Ghagus (23, 8.3) followed by Nicobari (14,
3.2) and WLH (10 and 2.2) breeds. The size of alleles ranged from 193 to 489 bp in Ghagus, 193 to 552 bp in Nicobari and 241 to 565 bp in the WLH breed. The
number of private alleles was also highest in Ghagus (18) followed by
Nicobari (8) and WLH (5) breeds. The most frequent allele was 261 bp in WLH
(66 %), 343 bp in Nicobari (50.4 %) and 309 bp in the Ghagus (28.15 %)
breed. Observed and expected heterozygosities were highest in Ghagus (0.83,
0.88) followed by Nicobari (0.58, 0.68) and WLH (0.53, 0.54). The genetic
distance (Nei) between Ghagus and Nicobari breeds (2.24) was higher as
compared to that of Ghagus and WLH (1.23) and that between Nicobari and WLH
breeds (0.89). Association analysis revealed significant influence of MHC
alleles on body weight, egg production in Ghagus and WLH breeds and antibody
titres to Newcastle disease vaccine in the Nicobari breed.
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Affiliation(s)
- Santosh Haunshi
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Divya Devara
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Kannaki Ramasamy
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
| | - Rajkumar Ullengala
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad 500030, India
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E GX, Duan XH, Yang BG, Na RS, Han YG, Zeng Y. Genetic Diversity Pattern of the MHC-LEI0258 Locus across Asian Populations of Chickens. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hemocytes transcriptome profile of the Chinese mitten crab (Eriocheir sinensis). AQUACULTURE AND FISHERIES 2018. [DOI: 10.1016/j.aaf.2018.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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