Genetic characteristics of Jiaji Duck by whole genome re-sequencing

Gu, Lihong; Feng, Wang; Lin, Zhemin; Xu, Tieshan; Lin, Dajie; Xing, Manping; Yang, Shuo; Chao, Zhe; Ye, Baoguo; Peng, Licong; Hui, Chunhui; Liu, Lizhi; Hou, Shuisheng

doi:10.1371/journal.pone.0228964

Cited by 11 publications

(9 citation statements)

References 51 publications

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“…Geographical isolation rarely allows genomic communication, and the traditional free-range breeding pattern results in low selection intensity. The diversity and origin of some Chinese domestic duck breeds have been studied using molecular markers, including mitochondrial DNA (mtDNA) ( Zhang et al 2007 ; He et al 2008 ; Li et al 2010b ), microsatellite markers ( Li et al 2006 , 2010a ; Liu et al 2008 ), and single-nucleotide polymorphisms (SNPs) ( Gu et al 2020 ; Wang et al 2020 ). However, most studies on Guangxi ducks focused on infectious diseases ( Xie et al 2012a , b ; Peng et al 2013 ), sequence data ( Zhang et al 2014 ; Xie et al 2016a , b ; Zhang et al 2016 ) or only contained a few Guangxi duck breeds in their breed categories ( Liu et al 2008 ; Li et al 2010b ; Zhou et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

Wang

Sun

et al. 2021

G3 Genes|Genomes|Genetics

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Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity (Hp), nucleotide diversity (π), Tajima’s D, and FST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.

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Section: Introductionmentioning

confidence: 99%

Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

Wang

Sun

et al. 2021

G3 Genes|Genomes|Genetics

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“…We found that two interferon genes ( IFNAR1 and IFNAR2 ) were simultaneously involved in these four pathways and that the tumor necrosis factor (TNF) gene and a TLR5 gene were independently involved in the Cytokine signaling pathway and the Toll-like receptor pathway, respectively (Additional file 15 : Table S12). Gu et al [ 26 ] also found that IFNAR1 and TLR5 exhibited Muscovy-specific SNPs. Signatures of positive selection and species-specific SNPs both indicated that these two Muscovy duck genes underwent adaptive evolution.…”

Section: Resultsmentioning

confidence: 99%

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses

et al. 2021

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Background The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity. Results We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the “faster-Z effect” of chromosome evolution. Conclusions The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses.

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“…Sample Size = number of genotypes sequenced. Species Sample size Premature stops Synonymous Non-synonymous Citation Ananas comosus 89 7,084 689,019 589,484 (Chen et al 2019 ) Arabidopsis thaliana 1,135 27,813 803,665 1,135,115 (1001 Genomes Consortium 2016 ) Bos indicus 20 1,132 255,296 155,251 (Iqbal et al 2019 ) Bos taurus 15 3,837 1,155,244 524,103 (Zhang et al 2019 ) Branchiostoma belcheri 20 11,487 2,818,189 1,467,863 (Bi et al 2020 ) Brassica napus 991 1,413 120,926 79,018 (Wu et al 2019 ) Caenorhabditis elegans 330 5,084 271,950 261,538 (Cook et al 2017 ) Cairina moschata 15 285 36,517 19,817 (Gu et al 2020 ) Canis lupus 722 11,273 540,063 332,559 (Plassais et al 2019 ) Capsella grandiflora 15 5,209 644,326 478,238 (Koenig et al 2019 ) Capsella orientalis 16 269 11,250 13,281 (Koenig et al 2019...…”

Section: The Historical Contextmentioning

confidence: 99%

The population genomics of adaptive loss of function

et al. 2021

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Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

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Genetic characteristics of Jiaji Duck by whole genome re-sequencing

Cited by 11 publications

References 51 publications

Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses

The population genomics of adaptive loss of function

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