Genetic differentiation and identification of key genes related to biomineralization and coloration in three Hyriopsis cumingii strains exhibiting different inner shell colors

Honghui Hu; Zhiyan Wang; Liang Jia; Hao Wang; Xuenan Li; Gaolun Lv; Zhiyi Bai; Jiale Li

Aquaculture Reports (Apr 2024)

Genetic differentiation and identification of key genes related to biomineralization and coloration in three Hyriopsis cumingii strains exhibiting different inner shell colors

Honghui Hu,
Zhiyan Wang,
Liang Jia,
Hao Wang,
Xuenan Li,
Gaolun Lv,
Zhiyi Bai,
Jiale Li

Affiliations

Honghui Hu: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Zhiyan Wang: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Liang Jia: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Hao Wang: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Xuenan Li: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Gaolun Lv: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China
Zhiyi Bai: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Corresponding authors at: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
Jiale Li: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Corresponding authors at: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China

Journal volume & issue: Vol. 35
p. 101939

Abstract

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Hyriopsis cumingii is one of the most popular freshwater mussels for the pearl culture industry in China. Three elite strains, i.e., Shenzi No. 1 (purple inner shell, SZ1), Shenzhe No. 3 (white inner shell and rapid growth, SZ3), and Golden strain (golden inner shell, GS), exhibit advantageous characteristics in terms of pearl coloration and biomineralization, which result in a significantly higher pearl quality. To explore the genetic basis of phenotypic variation, the three populations were subjected to whole-genome resequencing. A total of 38,781,748 high quality single nucleotide polymorphisms (SNPs) were identified across the genomes of the three strains. The three populations exhibited high levels of genetic diversity of individuals within each population, as expressed by high heterozygosity (Ho: 0.3099–0.3170, He: 0.2969). The GS population appeared to have experienced a greater selective pressure than SZ1 and SZ3, as denoted by its higher linkage disequilibrium (LD) level. By combining the pairwise comparison of the fixation index (Fst) and nucleotide diversity ratio (θπ), we identified four critical biomineralization-related genes (CaM, CHST, CHSY, and COL6A3) and three color-related genes (TRY, FER, and BCO1) that may serve as selective signatures for the breeding of H. cumingii. In summary, the identified functional genes as well as their corresponding SNP loci provided a genetic basis for selecting traits related to inner shell color and biomineralization and may accelerate the progress of marker-assisted selection in H. cumingii.

Published in Aquaculture Reports

ISSN: 2352-5134 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture: Aquaculture. Fisheries. Angling
Website: http://www.journals.elsevier.com/aquaculture-reports/

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