Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)OACSTPCD
The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.
Shao-Xuan Wu;Qi-Fan Zeng;Wen-Tao Han;Meng-Ya Wang;Hui Ding;Ming-Xuan Teng;Ming-Yi Wang;Pei-Yu Li;Xin Gao;Zhen-Min Bao;Bo Wang;Jing-Jie Hu
MOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,China Hainan Seed Industry Laboratory,Sanya,Hainan 572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,China Hainan Seed Industry Laboratory,Sanya,Hainan 572025,China Southern Marine Science and Engineer Guangdong Laboratory,Guangzhou,Guangdong 511458,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,China Hainan Seed Industry Laboratory,Sanya,Hainan 572025,ChinaMOE Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province,Sanya Oceanographic Institution,Ocean University of China,Qingdao,Shandong/Sanya,Hainan 266100/572025,China Hainan Seed Industry Laboratory,Sanya,Hainan 572025,China Southern Marine Science and Engineer Guangdong Laboratory,Guangzhou,Guangdong 511458,China
水产学
Plectropomus leopardusWhole-genome resequencingGrowthHaplotype reference panelSingle nucleotide polymorphisms
《Zoological Research》 2024 (2)
P.329-340,12
supported by the National Key Research and Development Program of China (2022YFD2400501)Key R&D Project of Hainan Province (ZDYF2021XDNY133)Project of Sanya Yazhouwan Science and Technology City Management Foundation (SKJC-2020-02-009)PhD Scientific Research and Innovation Foundation of Sanya Yazhou Bay Science and Technology City (HSPHDSRF-2022-02-007)Young Elite Scientists Sponsorship Program by CAST (2023QNRC001)。
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