Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows

Zhang, Hailiang; Mi, Siyuan; Brito, Luiz F.; Hu, Lirong; Wang, Lei; Ma, Longgang; Xu, Qiyou; Guo, Gang; Yu, Ying; Wang, Yachun

doi:10.1016/j.jgg.2023.01.011

Cited by 7 publications

(3 citation statements)

References 82 publications

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“…However, the quantitative traits of beef cattle are co-regulated by multiple genes, which are harder to find. GWAS provides a good example of screening for dominant genes associated with quantitative traits in livestock and poultry, such as pigs [24,25], chickens [26][27][28], ducks [29], sheep [30,31], beef cattle [32,33], and cows [34][35][36]. Moreover, GWASs of beef cattle mainly assess growth traits [37], reproductive traits [38,39], and meat quality traits [40,41].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

Yu,

Guo

et al. 2023

Animals

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A genome-wide association study (GWAS) is an effective tool for identifying the dominant genes of complex economic traits in livestock by statistical analysis of genotype data and measured phenotype data. In this study, we rigorously measured 14 body conformation traits in 254 Qinchuan cattle, comprising body weight (BW), body height (BOH), back height (BAH), buttock height (BUH), chest depth (CD), chest width (CW), hip cross height (HCH), body length (BL), hip width (HW), rump length (RL), pin bone width (PBW), chest girth (CG), abdomen circumference (AG), and calf circumference (CC). After quality control, 281,889 SNPs were generated for GWAS with different traits. A total of 250 suggestive SNPs (p < 3.54 × 10−6) were screened and 37 candidate genes were annotated. Furthermore, we performed a linkage disequilibrium analysis of SNP loci and considered published studies, identifying the eight genes (ADAMTS17, ALDH1A3, CHSY1, MAGEL2, MEF2A, SYNM, CNTNAP5, and CTNNA3) most likely to be involved in growth traits. This study provides new insights into the regulatory mechanisms of bovine body size development, which can be very useful in the development of management and breeding strategies.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

Yu,

Guo

et al. 2023

Animals

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“…Only SNPs with MAF ≥ 0.01 [ 70 – 72 ] and missing rate ≤ 0.1 in a population were used for GWAS. Efficient Mixed-Model Association eXpedited program (EMMAx) was used for GWAS analysis [ 73 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

He,

Zhang,

Shi

et al. 2024

Genome Biol

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Background Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. Results Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. Conclusions This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

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“…These second messengers regulate various processes that affect cell growth, differentiation, and gene expression. A GWAS for 22 milk fatty acids in 784 Chinese Holstein cows showed associations of the ARS-BFGL-NGS-110475 in gene PLCE1 with monounsaturated and polyunsaturated fatty acid traits (MUFA and PUFA) and indices of fatty acid traits [64], BovineHD2600004009 with milk yield by multibreed genome-wide association [65], rs42816577 with subcutaneous fat deposition traits in Holstein cattle [66], and rs41624917 with fat percentage [44].…”

Section: Candidate Genes With Predicted Functionsmentioning

confidence: 99%

Overview of SNPs Associated with Trans Fat Content in Cow’s Milk

2023

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Lipids consumed with milk derivatives are one of the main parts of the human diet. Trans fatty acids in milk are causing a debate about their impact on the incidence of cardiovascular disease, pathological abnormalities, and cancer. The fatty acid profile of milk is influenced by a large number of different factors, one of which is genetic. The development of genetic studies, including Genome-Wide Association Studies (GWAS), may help define genomic regions associated with fatty acid content in milk, including trans fatty acids. This article provides an overview of international studies on the identification of genomic regions and SNPs associated with the trans fatty acids in cow’s milk. The results are based on research of cattle such as Norwegian Red cattle, Holstein, Jersey, and Brown Swiss. The presented review shows that 68 SNPs were localized on chromosomes 1, 2, 4–6, 8–10, 12, 14–20, 22–25, and 27–29. Further research in this direction will provide new information that will serve as an impetus for the creation of modern breeding technologies and increase the performance of the manufacture of high-quality dairy products. The search for genetic markers associated with the content of TFA in milk is a promising direction in agricultural science and will allow more complete breeding work with cattle.

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Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows

Cited by 7 publications

References 82 publications

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

Overview of SNPs Associated with Trans Fat Content in Cow’s Milk

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