Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes

Ma, Xiaoming; Chen, Jia; Fu, Donghai; Chen, Min; Ding, Xuezhi; Wu, Xiaoyun; Guo, Xian; Pei, Jie; Bao, Pengjia; Liang, Chunnian; Yan, Ping

doi:10.3390/genes10060463

Cited by 15 publications

(13 citation statements)

References 53 publications

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“…Our results show that the efficiency of the method depends on the type of genotype data. This is consistent with the findings of Xiaoming et al (2019) and of Wu et al (2014). In this study, we discovered 42 significant SNPs via singlemarker analyses; six erythrocyte traits were involved, including RBC, HGB, HCT, MCH, MCHC, and RWD_CV.…”

Section: Discussionsupporting

confidence: 89%

Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

et al. 2020

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Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.

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Section: Discussionsupporting

confidence: 89%

Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

et al. 2020

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“…RBCs are essential for oxygen transport within the organism and the removal of the byproducts of respiration. The platelets play an important role in blood coagulation, wound healing, inflammatory response, and organ transplant rejection [34]. The white blood cell has emerged as a marker of inflammation that is widely available in clinical practice [35].…”

Section: Discussionmentioning

confidence: 99%

A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus

Guo

Liang

et al. 2020

Animals

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Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.

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“…The phenotypic traits of the 18-month-old yak reference population were obtained in October 2018, including direct measurement of performance data, withers height, body length, body weight, chest girth (WH, BL, BW, CG) and eight hematological traits obtained from non-anticoagulated blood, namely, red blood cell count, hemoglobin, hematocrit, platelet count, lymphocyte count, medium white blood cell count, distribution of platelet width, and mean platelet volume (RBC, HGB, HCT, PLT, LYM, OTHR, PDW, and MPV), as described in a previous study [15]. Twelve phenotypic traits were tested for normality and those values falling more than 3 standard deviations from the mean were removed using SAS (version 9.2) (SAS Institute INC, North Carolina, NC, USA) [17].…”

Section: Methodsmentioning

confidence: 99%

“…In a previous study, a number of SNP loci associated with eight hematological traits were explored through GWAS [15]. Differing from the assumption of Bayes A, the assumption of Bayes B is that a small number of SNP loci have an effect but the majority of loci do not, across the whole genome [26].…”

Section: Methodsmentioning

confidence: 99%

“…), single step BLUP (ssBLUP), and other algorithms were considered for genomic selection and prediction [14]. In this study, three statistical methods (GBLUP, Bayes B, and Bayes Cπ) were selected for the prediction of the GEBV of four growth traits and eight hematological traits according to previous genome-wide association analysis (GWAS) results [15].…”

Section: Introductionmentioning

confidence: 99%

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A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)

Chen

et al. 2019

Animals

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Simple SummaryThe domesticated yak is among the most important livestock species on the Qinghai-Tibet Plateau. Breeders have the task of developing varieties that provide growth performance and disease resistance. Traditional breeding processes rely on complete family pedigree information and large numbers of data records. However, there are inevitably records that are missing, including incomplete pedigrees and long-term data tracking, resulting in prolonged breeding cycles, reduced breeding efficiency, and the lack of economic benefit. Genome selection (GS), also known as whole genomic selection (WGS), can significantly reduce the selection cycle of quantitative traits and accelerate genetic progression while displaying appropriate prediction accuracy (PA). It combines a reference population and single nucleotide polymorphism (SNP) loci rather than pedigrees to estimate the effect of all SNPs. Then breeding values of target traits are predicted. The key for GS is genomic prediction (GP) and an assessment of PA.AbstractThe aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools.

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Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes

Cited by 15 publications

References 53 publications

Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus

A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)

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