Construction of a Genetic Linkage Map Based on SNP Markers, QTL Mapping and Detection of Candidate Genes of Growth-Related Traits in Pacific Abalone Using Genotyping-by-Sequencing

Abstract

Pacific abalone (Haliotis discus hannai) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. It is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for its molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated and 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map of each growth-related trait. Both QTLs were located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that these identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.

Hdh-Tektin-4 Regulates Motility of Fresh and Cryopreserved Sperm in Pacific Abalone, Haliotis discus hannai

“…The qRT-PCR assay was conducted using a 2×qPCRBIO SyGreen Mix Lo-Rox kit (PCR Biosystems Ltd., UK), as described previously ( Kho et al, 2021 ). The qRT-PCR reaction mixture was prepared with cDNA template (1 μl), 10 pmol forward and reverse primer (1 μl each), SyGreen Mix (10 μl), and ultra-pure water (10 μl) in a total volume of 20 μl.…”

Identification and Characterization of Hdh-FMRF2 Gene in Pacific Abalone and Its Possible Role in Reproduction and Larva Development

“…The qRT-PCR assay was conducted using the 2× qPCRBIO SyGreen Mix Lo-ROX kit (PCR Biosystems Ltd., London, UK) as previously described [31]. A 20 µL of qRT-PCR reaction mixture was prepared using 1 µL of cDNA template, 1 µL of each gene specific forward and reverse primer, 10 µL of SyGreen Mix, and 7 µL of DDW.…”

Age-Dependent Growth-Related QTL Variations in Pacific Abalone, Haliotis discus hannai

“…At present, the entire abalone aquaculture industry uses hatchery-produced abalone seed. Abalone hatcheries produce seeds using conventional selection breeding [7]. Conventional phenotypical selection breeding substantially improves the growth rate of abalone.…”

“…Molecular and marker-assisted breeding is successfully used in many aquaculture species including greenshell mussel [9], Pacific oyster [10], noble scallop [11], whiteleg shrimp [12], salmon [13], Japanese flounder [14], and rainbow trout [15] to achieve higher growth and disease resistance. Regarding abalone, several studies performed genetic analysis and concluded that growth-related traits can be improved using MAS breeding [7,16]. However, the development of potential markers for growth-related traits across ages in abalone has not yet been studied.…”

“…Growth-related QTL studies have been performed on several commercially important molluscan species, including the Pacific abalone [7,16], small abalone [26], blacklip abalone [27], Manila clam [28], Pacific oyster [29], and bay scallop [30]. On the other hand, QTL variations across ages and families have been reported in several mammals and fishes, including the gilthead seabream [23], blackface sheep [24], nine-spined stickleback [31], chicken [32], and common carp [33].…”