Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Animal Genetics - Tập 49 Số 5 - Trang 483-487 - 2018
Liang Ma1, Zongli Li2, Yong Cai3, Hongwei Xu3, Ruolin Yang2, Xianyong Lan1
1Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
2College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
3Science Experimental Center, Northwest University for Nationalities, Lanzhou, Gansu, 730030 China

Tóm tắt

SummaryThe identification of genetic variations underlying desired phenotypes is one of the main challenges of current livestock genetic research. High‐throughput transcriptome sequencing has been recognized as an efficient way to unravel the rich genetic variants across various species. The Lanzhou Fat‐Tail sheep is an endangered sheep breed in China with a notable feature of an exaggerated fat tail that also independently occurs in other sheep breeds. However, the genetic mechanism underlying this particular trait has not been fully elucidated yet. In this study, we used RNA‐seq on tissue samples (longissimus dorsi muscle, perinephric fat and tail fat) from three sheep breeds with either fat or thin tails and characterized the genetic variation in Lanzhou Fat‐Tail sheep with the ultimate goal of identifying the causal genes and genetic networks responsible for the fat tail in this rare sheep breed. In total, 7 122 920 SNPs and 901 518 indels were detected in the nine individual sheep investigated, of which 606 952 SNPs (8.5%) and 77 633 indels (8.6%) overlapped with QTL associated with fat traits in sheep. Furthermore, we detected 26 613 specific SNPs in Lanzhou Fat‐Tail sheep and 44 SNPs located in the same genomic position reported in another sheep breed with fat tails. Interestingly, 33 SNPs are selectively distributed on a chromosome 3 region (39.58–40.91 Mb) that was reported as a strong candidate genomic region for fat deposition in tails of sheep. Our research has also suggested that three genes (CREB1, WDR92 and ETAA1) may be associated with fat tail development. In summary, the resultant genetic variants data in this study provide a valuable resource for marker‐assisted selection of the trait in Lanzhou Fat‐Tail sheep populations.

Từ khóa


Tài liệu tham khảo

AndrewsS.(2012)fastqc: a quality control tool for high throughput sequence data.Babraham Bioinformatics.http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

10.1051/animres:2004012

10.1038/ng.806

10.1093/nar/gkv1233

10.1038/s41598-017-14967-9

10.1016/j.smallrumres.2005.01.001

10.1038/nmeth.3317

10.1080/19336896.2017.1300740

10.1080/19336896.2017.1405886

10.1371/journal.pgen.1003681

10.2527/jas.2015-9389

10.1186/1471-2156-13-10

10.1038/sj.onc.1208331

10.1093/nar/gkq603

10.1016/j.gene.2014.07.072

WysokerA. TibbettsK. McCowanM. HomerN.&FennellT.(2010)picard.http://broadinstitute.github.io/picard/.

10.1111/age.12572

10.1111/age.12477

Thông tin
Thông tin xuất bản

Animal Genetics

Tập 49 Số 5

483-487

Thông tin tác giả