Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus
SAWAR KHAN XIAOCHAO ZHAO YINI HOU CHUNXIU YUAN YUMEI LI XIAOPING LUO JIANZHI LIU XINGANG FENG
Click here to view fulltext PDF
Permanent link:
https://www.ias.ac.in/article/fulltext/jbsc/044/04/0097
The parasitic nematode Haemonchus contortus is one of the world’s most important parasites of small ruminants that causessignificant economic losses to the livestock sector. The population structure and selection in its various strains are poorlyunderstood. No study so far compared its different populations using genome-wide data. Here, we focused on differentgeographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK andAustralia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure andselection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, andidentified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB,82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (p =0.0092–0.0133) within each strain, and a significant differentiation level (average Fst = 0.34264) among them. Chinesepopulations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HBshowed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) privateselective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selectivesweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing canbe used to assess the signature of selection in H. contortus.
SAWAR KHAN1 XIAOCHAO ZHAO1 YINI HOU1 2 CHUNXIU YUAN1 YUMEI LI1 2 XIAOPING LUO1 3 JIANZHI LIU4 XINGANG FENG1
Volume 45, 2020
All articles
Continuous Article Publishing mode
Click here for Editorial Note on CAP Mode
© 2021-2022 Indian Academy of Sciences, Bengaluru.