Page 227 - 《水产学报》2023年第1期

刘绵宇，等 水产学报, 2023, 47(1): 019417

Application of the liquid chip "Yellow Sea Chip No.1" in genetic evaluation of
the base population with resistance to acute hepatopancreatic
necrosis disease in Litopenaeus vannamei

2
2
2
2
2
1,2
LIU Mianyu , LI Xupeng , KONG Jie , MENG Xianhong , CHEN Meijia , LUO Kun ,
2
2
2
2
2
2
SUI Juan , DAI Ping , ZHANG Yawen , QIANG Guangfeng , TAN Jian , CHEN Baolong ,
2
1
3
CAO Jiawang , LI Bobo , LAI Xiaofang , LUAN Sheng 2*
(1. Key Laboratory of Marine Biological Resources and Environment of Jiangsu Province, College of Marine Science and Fisheries,
Jiangsu Ocean University, Lianyungang 222005, China;
2. Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs; Laboratory for
Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao);
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
3. BLUP Aquabreed Co., Ltd., Weifang 261312, China)
Abstract: To evaluate the application potential of single nucleotide polymorphism(SNP) chip in the construction
of the base population for breeding, three different populations (EE, PP and SS) of Litopenaeus vannamei were
challenged by Vibrio parahaemolyticus (Vp AHPND ), and the genomic information of 146 samples was obtained
using the independently developed 40K SNP liquid chip “Yellow Sea Chip No.1”. The genetic background
was systematically investigated and acute hepatopancreatic necrosis disease (AHPND) resistance of popula-
tions was estimated. The Vp AHPND challenge test indicated that there were differences in disease resistance
between different populations. When the overall mortality was more than 50%, the survival rate of PP population
was 12.9% and 11.6% higher than that of EE and SS populations, respectively. The phylogenetic tree was con-
structed by using 38 148 SNP markers after quality control. The result showed that the individuals of the same fam-
ily first clustered together, and then the multiple families of the same population clustered together. Principal com-
ponent analysis and genetic structure analysis also implied that the 146 individuals could be accurately divided into
3 groups, which was consistent with the phylogenetic tree. The analysis of genetic diversity for three populations
showed that the average value of observed heterozygosity (H ) was 0.25-0.29. The average value of polymorphic
o
information content (PIC) was 0.20-0.23. The differences on the above three parameters between three popula-
tions were very significant (P < 0.01). The coefficient of genetic differentiation (F ) among the three populations
ST
was 0.11-0.21, indicating that there was medium-high level of genetic differentiation. Genomic inbreeding ana-
lysis showed that the average inbreeding coefficients of EE, PP and SS populations were −0.05±0.06, 0.20±0.09
and 0.37±0.07, respectively. Some individuals of PP and EE populations showed high levels of inbreeding. Using
single step genomic BLUP with metafounder(sssGBLUP-MF) model with genotype, phenotype and pedigree
information, the estimated heritability of survival after Vp AHPND infection was medium (0.24±0.07), indicating that
the base population had a promising breeding potential. To summarize, the efficiency of constructing and evaluat-
ing the base population can be further enhanced by using the liquid chip "Yellow Sea Chip No.1".
Key words: Litopenaeus vannamei; base population; AHPND; SNP chip; genetic diversity

Corresponding author: LUAN Sheng. E-mail: luansheng@ysfri.ac.cn
Funding projects: Central Public-interest Scientific Institution Basal Research Fund (No. 20603022020003); Sci-
ence and Technology Innovation Team project of Chinese Academy of Fishery Sciences (2020TD26); Major
Applied Technology Innovation Project of agriculture in Shandong Province (No. SD2019YY001); Scientific
Research Project of Academician Innovation platform in Hainan Province (YSPTZX202104); Talent Team bid-
ding Project of Marine Equipment and Marine Biology in Zhanjiang (2021E05032); Supported by China Agricul-
ture Research System (CARS-48)

https://www.china-fishery.cn 中国水产学会主办 sponsored by China Society of Fisheries
10