Identification of 19 loci for reproductive traits in a local Chinese chicken by genome-wide study

Fan, Qunping; Wu, Pengcheng; G, Dai; Zhang, G X; Zhang, T; Qin, Xue; Shi, Huitong; Wang, J Y

doi:10.4238/gmr16019431

Cited by 20 publications

(15 citation statements)

References 32 publications

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“…goat (An et al, 2015a,b), such evidence suggested KIT may be the most promising gene for large LS. Another, KCNH7 also had been found to be significantly associated with animal reproductive traits (Fan et al, 2017). Besides, KMT2E, termed as MLL5, had been demonstrated to be required for normal spermatogenesis, its knockout mouse showed a post meiotic phenotype and infertile (Heuser et al, 2009;Yap et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

et al. 2020

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Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima's D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.

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Section: Discussionmentioning

confidence: 99%

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

et al. 2020

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“…Liu et al (28) confirmed SLIT2 as a candidate gene associated with muscle weight in an F2 resource chicken population and with female fertility in Nordic Red cattle (25). Two SNPs (BovineHD-0600010716 and BovineHD0600010701) associated with SW are located in FAM184B (family with sequence similarity, member B), a gene previously identified to be associated with adult height in human (22), osteochondrosis lesions in French Trotters (58), carcass and meat quality traits in Duroc pigs (18), reproductive traits in a local Chinese chicken, and locomotive traits in Purebred Spanish horses (15,46). Four SNPs associated with SW are located in LAP3 (Leucine aminopeptidase 3), which showed different expression levels over the different stages of the lactogenic cycle in cattle mammary biopsy (47).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

Xia

Chang

et al. 2018

Physiological Genomics

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Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

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“…Based on multiple previous reports [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33], we have chosen 14 characteristic SNP markers strongly associated with growth traits or carcass traits (P < 0.05) including rs13687128, rs317360945, rs14734533, rs314127605, NC_ 006092.4: g.25657391 T > A, NT_464126.1: g.66916G > A, rs314901473, rs316142388, rs314403820, rs14202565, rs16438236, rs13939265, rs15620544, rs16434462 and 14 characteristic SNP markers with strongly association with egg production traits (P < 0.05) including NC_006127.4: g.24021190G > A, rs16349546, NC_006096.4: g22545152 G > C, rs16486559, rs317328077, rs14714701, rs14085822, rs13905010, rs15602813, rs14491030, rs14699480, rs14652932, rs315420959 and rs313187645 for genotype frequency analysis. The specific information of the SNP markers is given together with their genetic background and corresponding traits in Tables 1 and 2.…”

Section: Selection and Summary Of 28 Snp Markersmentioning

confidence: 99%

“…To characterize the genetic variations and genetic relationships among different populations using DNA markers, a total of 28 identified SNP markers, including 14 growth or carcass traits associated loci and 14 egg laying related genome positions, were selected from the previous reports [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. By using the MassArray technology, an Agena Bioscience MassARRAY System which is capable of efficiently genotyping tens to hundreds of SNPs with high accuracy, we detected the genotype frequency distributions of the 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line [34,35].…”

Section: Introductionmentioning

confidence: 99%

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

Zhang

Ren

et al. 2020

BMC Genet

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Background: Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Results: Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line. Conclusions: Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations.

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Identification of 19 loci for reproductive traits in a local Chinese chicken by genome-wide study

Cited by 20 publications

References 32 publications

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

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