Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens

Liu, Zhuang; Sun, Chang; Yan, Yong-Bin; Li, Guangqi; Li, Xiao Chang; Wu, Guiqin; Yang, Ning

doi:10.1016/j.psj.2021.101044

Cited by 16 publications

(11 citation statements)

References 33 publications

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“…GBTS technology, with its high sequencing depth (>200×), ensures accurate genotyping. Solid‐phase chips generally exhibit SNP detection rates below 95% in local chicken populations; however, this chip achieved a target site detection rate as high as 99.8%, with significantly greater polymorphism than other chips (average MAF = 0.39 compared to 0.15–0.27 for other chips) [13, 19]. Furthermore, the GBTS technology detects target sites as well as the variants around them.…”

Section: Discussionmentioning

confidence: 99%

“…GBTS technology has been extensively applied to animals and plants, including maize [6], soybean [7], broccoli [8], and sheep [9]. Although several solid‐phase SNP chips have been developed for chickens, primarily based on high‐producing broiler or layer breeds, containing 50,000–500,000 SNP loci, such as the Illumina 60 K [10], Affymetrix 600 K [11] and 55 K [12], and Phenoix Chip‐I [13], they have some limitations in conducting genetic resource research and breeding of local chicken breeds in China. These limitations include insufficient polymorphisms, lack of functional markers, and high costs.…”

Section: Introductionmentioning

confidence: 99%

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Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Animal Research and One Health

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Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid‐phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high‐quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome‐wide association study of broilers, resulting in the identification of several growth‐ and meat quality‐related loci. Therefore, the newly developed chip is efficient, cost‐effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Animal Research and One Health

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“…With the increasing availability of whole-genome sequence data in recent years, there has been an evolving trend toward screening causal mutations or variants in high LD with causative mutations for multiple traits and using them to design customized SNP panels for driving genetic improvements for traits in livestock ( Liu et al, 2021 ; Xiang et al, 2021 ). As noted earlier, Xiang et al (2021) developed a custom SNP array (called “XT-50K” array) that includes potential causative mutations discovered from dairy cattle across 34 traits, representing milk production, fertility, type, and management.…”

Section: Understanding the Biology Of Thermal Stress: Study Traits An...mentioning

confidence: 99%

Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions

et al. 2022

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Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.

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“…The Beijing You chicken is a traditional Chinese indigenous breed with head crest, beard and fuzzy shank, which produced much less egg mass compared to the White Leghorn. These two breeds have previously been reported genetically distant ( 22 ), and this would contribute the heterosis of traits. The transcriptome analysis of the ovary in purebreds and crossbreeds was implemented to reveal the key lncRNAs and genes regulating the formation of sexual maturation heterosis.…”

Section: Introductionmentioning

confidence: 97%

Genetic Basis of Sexual Maturation Heterosis: Insights From Ovary lncRNA and mRNA Repertoire in Chicken

et al. 2022

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Sexual maturation is fundamental to the reproduction and production performance, heterosis of which has been widely used in animal crossbreeding. However, the underlying mechanism have long remained elusive, despite its profound biological and agricultural significance. In the current study, the reciprocal crossing between White Leghorns and Beijing You chickens were performed to measure the sexual maturation heterosis, and the ovary lncRNAs and mRNAs of purebreds and crossbreeds were profiled to illustrate molecular mechanism of heterosis. Heterosis larger than 20% was found for pubic space and oviduct length, whereas age at first egg showed negative heterosis in both crossbreeds. We identified 1170 known lncRNAs and 1994 putative lncRNAs in chicken ovary using a stringent pipeline. Gene expression pattern showed that nonadditivity was predominant, and the proportion of nonadditive lncRNAs and genes was similar between two crossbreeds, ranging from 44.24% to 49.15%. A total of 200 lncRNAs and 682 genes were shared by two crossbreeds, respectively. GO and KEGG analysis showed that the common genes were significantly enriched in the cell cycle, animal organ development, gonad development, ECM-receptor interaction, calcium signaling pathway and GnRH signaling pathway. Weighted gene co-expression network analysis (WGCNA) identified that 7 out of 20 co-expressed lncRNA-mRNA modules significantly correlated with oviduct length and pubic space. Interestingly, genes harbored in seven modules were also enriched in the similar biological process and pathways, in which nonadditive lncRNAs, such as MSTRG.17017.1 and MSTRG.6475.20, were strongly associated with nonadditive genes, such as CACNA1C and TGFB1 to affect gonad development and GnRH signaling pathway, respectively. Moreover, the results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. Integrated with positive heterosis of serum GnRH and melatonin content detected in crossbreeds, we speculated that nonadditive genes involved in the GnRH signaling pathway elevated the gonad development, leading to the sexual maturation heterosis. We characterized a systematic landscape of ovary lncRNAs and mRNAs related to sexual maturation heterosis in chicken. The quantitative exploration of hybrid transcriptome changes lays foundation for genetic improvement of sexual maturation traits and provides insights into endocrine control of sexual maturation.

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Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens

Cited by 16 publications

References 33 publications

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions

Genetic Basis of Sexual Maturation Heterosis: Insights From Ovary lncRNA and mRNA Repertoire in Chicken

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