基于液相芯片"黄海芯1号"55K SNP信息开展凡纳滨对虾收获体重的ssGWAS和FarmCPU分析
ssGWAS and FarmCPU analysis of harvest body weight using the liquid chip"Yellow Sea Chip No.1"with 55K SNPs in Litopenaeus vannamei
摘要
Abstract
Growth and survival tests were conducted on 74 families,comprising both selection and introduced pop-ulations with fast growth rates to identify single nucleotide polymorphisms(SNPs)and functional genes associ-ated with growth traits in Litopenaeus vannamei.High-throughput genotyping of individuals from 39 families was carried out using the"Yellow Sea Chip No.1"liquid chip,which included 55K SNPs.Genomic genetic parameters for harvest body weight were estimated using the ssGBLUP method.Additionally,the ssGWAS and FarmCPU methods were employed for the first time to discover potentially associated SNPs and candidate genes.The estima-tion of genetic parameters revealed a heritability of 0.47 for harvest body weight,indicating a moderate to high potential for genetic improvement within the population.The ssGWAS and FarmCPU analyses identified two and six genome-wide significant SNPs(P<1.26×10-6),respectively,explaining phenotypic variation ranging from 2.71%to 6.76%.A common SNP was also identified among them.Furthermore,both methods separately screened nine and 14 suggestive genome-wide SNPs(P<2.523×10-5),explaining phenotypic variation ranging from 1.33%to 6.76%.QQ plots demonstrated that FarmCPU exhibited superior control over false positives compared to ssGWAS.Gene annotation of the seven significantly associated SNPs revealed 15 candidate genes related to func-tions such as the nervous system,muscle development,and energy metabolism.Notably,the common signific-antly associated SNP was annotated to two genes:LOC113809777,which encoded a hydrolase promoting glyco-gen hydrolysis,and LOC113809778,a transcriptional regulatory factor associated with gene expression regulation.In conclusion,utilizing the"Yellow Sea Chip No.1"liquid chip,the ssGWAS and FarmCPU methods facilitated the identification of significantly associated SNPs with harvest weight in L.vannamei,offering valuable insights into the genetic basis of growth traits.关键词
凡纳滨对虾/ssGWAS/FarmCPU/体重/显著关联SNP位点Key words
Litopenaeus vannamei/ssGWAS/FarmCPU/body weight/significant SNP分类
农业科技引用本文复制引用
夏岩,代平,曹家旺,谭建,强光峰,刘绵宇,栾生,孔杰,王平,傅强,罗坤,陈宝龙,隋娟,周浩,孟宪红..基于液相芯片"黄海芯1号"55K SNP信息开展凡纳滨对虾收获体重的ssGWAS和FarmCPU分析[J].水产学报,2024,48(12):40-50,11.基金项目
国家重点研发计划(2022YFD2400202) （2022YFD2400202）
中国水产科学研究院科技创新团队(2020TD26) （2020TD26）
现代农业产业技术体系专项(CARS-48) （CARS-48）
广东省"十四五"广东省农业科技创新十大主攻方向"揭榜挂帅"项目(2022SDZG01) （2022SDZG01）
泰山学者工程 （）
山东省重点研发计划(农业良种工程)(2024LZGC038) National Key Research and Development Program of China(2022YFD2400202) （农业良种工程）
Science and Technology Innovation Team Project of Chinese Academy of Fishery Sciences(2020TD26) （2020TD26）
China Agriculture Research System(CARS-48) （CARS-48）
The Open Competition Program of Top Ten Critical Priorities of Agricultural Sci-ence and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG01) （2022SDZG01）
Taishan Scholars Program （）
Shandong Province Key R&D Program(Agricultural Breeding Project)(2024LZGC038) （Agricultural Breeding Project）
