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https://www.ias.ac.in/article/fulltext/jbsc/044/04/0097

2b-RAD sequencing; genome-wide SNP analysis; Haemonchus contortus; selective sweeps; signature of selection

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 HOU^{1 2} CHUNXIU YUAN¹ YUMEI LI^{1 2} XIAOPING LUO^{1 3} JIANZHI LIU⁴ XINGANG FENG¹

1. Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, People’s Republic of China
2. College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 250014, People’s Republic of China
3. College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, Inner Mongolia Autonomous Region, People’s Republic of China
4. Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, Tibet Autonomous Region, People’s Republic of China

Published

1 September 2019

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