INDEL and SNP density in each chromosome.

<p>Densities were calculated as the number per 10 kb (INDEL) and kb (SNP), respectively. Densities are averaged by chicken individuals and corrected by read depth. Coverage was calculated based on Q20 reads.</p

Genome-Wide Characterization of Insertion and Deletion Variation in Chicken Using Next Generation Sequencing

<div><p>Insertion and deletion (INDEL) is one of the main events contributing to genetic and phenotypic diversity, which receives less attention than SNP and large structural variation. To gain a better knowledge of INDEL variation in chicken genome, we applied next generation sequencing on 12 diverse chicken breeds at an average effective depth of 8.6. Over 1.3 million non-redundant short INDELs (1–49 bp) were obtained, the vast majority (92.48%) of which were novel. Follow-up validation assays confirmed that most (88.00%) of the randomly selected INDELs represent true variations. The majority (95.76%) of INDELs were less than 10 bp. Both the detected number and affected bases were larger for deletions than insertions. In total, INDELs covered 3.8 Mbp, corresponding to 0.36% of the chicken genome. The average genomic INDEL density was estimated as 0.49 per kb. INDELs were ubiquitous and distributed in a non-uniform fashion across chromosomes, with lower INDEL density in micro-chromosomes than in others, and some functional regions like exons and UTRs were prone to less INDELs than introns and intergenic regions. Nearly 620,253 INDELs fell in genic regions, 1,765 (0.28%) of which located in exons, spanning 1,358 (7.56%) unique Ensembl genes. Many of them are associated with economically important traits and some are the homologues of human disease-related genes. We demonstrate that sequencing multiple individuals at a medium depth offers a promising way for reliable identification of INDELs. The coding INDELs are valuable candidates for further elucidation of the association between genotypes and phenotypes. The chicken INDELs revealed by our study can be useful for future studies, including development of INDEL markers, construction of high density linkage map, INDEL arrays design, and hopefully, molecular breeding programs in chicken.</p></div

Summary of sequencing and mapping statistics.

<p>*Chicken abbreviations: BY, Beijing You; CS, Cornish; DX, Dongxiang; LX, Luxi Game; RIR, Rhode Island Red; RJF, Red Jungle Fowl; SG, Shouguang; SK, Silkie; TB, Tibetan; WC, Wenchang; WL, White Leghorn; WR, White Plymouth Rock.</p

Distribution of INDEL length.

<p>INDELs with multiple genotypes were not included.</p

SNP to INDEL ratio.

<p>The ratios were plotted based on the non-redundant (Union) data and the data averaged by chickens (Average), respectively. A: SNP to INDEL ratio across chromosomes. B: SNP to INDEL ratios in functional categories.</p

Statistics of INDELs and SNPs in functional regions.

a<p>Regions that are 1 kb apart from the transcription start site.</p>b<p>Variant located in both upstream and downstream regions (possibly for two different genes).</p>c<p>Variants located in both 5′UTR and 3′UTR regions (possibly for two different genes).</p>d<p>Variants located in the transcripts without coding annotation in the current Ensembl gene annotation.</p>e<p>Variants caused gain or loss of stop codon.</p

Short INDELs detected in 12 diverse chicken breeds.

a<p>Chicken abbreviations: BY, Beijing You; CS, Cornish; DX, Dongxiang; LX, Luxi Game; RIR, Rhode Island Red; RJF, Red Jungle Fowl; SG, Shouguang; SK, Silkie; TB, Tibetan; WC, Wenchang; WL, White Leghorn; WR, White Plymouth Rock.</p>b<p>INDELs that have multiple genotypes were excluded.</p>c<p>Corrected for INDELs called in more than one individual.</p

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq

<div><p>Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.</p></div

The percentage of reads mapped to exonic, intronic and intergenic regions.

<p>The percentage of reads mapped to exonic, intronic and intergenic regions.</p

Summary statistics for sequence quality and alignment information of six samples.

<p>Q20 and Q30 represent the proportion of bases with a Phred quality score greater than 20 and 30, respectively.</p><p>Summary statistics for sequence quality and alignment information of six samples.</p