Yuttiwat Permkullaya, Sukhavachana Sila, Pattarapanyawong Naruechon, Phuthaworn Chontida, Poompuang Supawadee
Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand.
Andaman Coastal Research Station for Development, Faculty of Fisheries, Kasetsart University, Ranong, Thailand.
Mar Biotechnol (NY). 2025 Jul 15;27(4):111. doi: 10.1007/s10126-025-10489-y.
The aims of this study were to investigate marker-growth trait associations and construct a SNP-based linkage map for an Asian seabass (KU) population from Thailand. First, we performed GWAS using phenotypes (weight and length) and genotypes (25,647 SNPs) for 1100 390-day-old fish. We selected the top 70 SNPs with allele substitution effects, ranging from 6.84 to 81.91 g for weight and from 0.12 to 1.8 cm for length for further analyses. Cross-validation of 70 SNPs using GBLUP yielded breeding value prediction accuracies 0.65 to 0.70. Second, we utilized previously published genome-wide SNPs and mapping data from multiple populations and the KU data to predict the genetic linkage map for the KU population using the Marey map approach. The KU linkage map consisted of 24 chromosomes spanning 567 Mb, with average marker spacing of 0.07 cM. The number of markers ranged from 598 to 1334, with an average of 1099 markers per chromosome. The predicted local recombination rates varied from 4.76 to 43.40 cM/Mb with an average of 2.35 cM/Mb. Lastly, Kompetitive allele-specific PCR (KASP) markers were developed from 70 SNPs and validated in 200 fish. The KASP assays were successful for all 70 SNPs in 196 fish with SNP call rates of 98.2 to 100%. Fifty-eight SNPs were found to have segregated across the genome, except for chromosomes 23 and 24. The linkage map obtained in this study provides a framework for future QTL mapping of growth-related traits in the KU population.
本研究的目的是调查泰国亚洲海鲈（KU）群体中标记与生长性状的关联，并构建基于单核苷酸多态性（SNP）的连锁图谱。首先，我们对1100尾390日龄的鱼进行了全基因组关联研究（GWAS），使用了表型（体重和体长）和基因型（25,647个SNP）。我们选择了70个等位基因替代效应最高的SNP进行进一步分析，体重的效应范围为6.84至81.91克，体长的效应范围为0.12至1.8厘米。使用基因组最佳线性无偏预测（GBLUP）对70个SNP进行交叉验证，得出育种值预测准确率为0.65至0.70。其次，我们利用先前发表的全基因组SNP以及多个群体和KU群体的数据，采用Marey图谱法预测KU群体的遗传连锁图谱。KU连锁图谱由24条染色体组成，跨度为567兆碱基（Mb），平均标记间距为0.07厘摩（cM）。标记数量从598到1334不等，每条染色体平均有1099个标记。预测的局部重组率在4.76至43.40 cM/Mb之间，平均为2.35 cM/Mb。最后，从70个SNP开发了竞争性等位基因特异性PCR（KASP）标记，并在200尾鱼中进行了验证。196尾鱼中所有70个SNP的KASP检测均成功，SNP检出率为98.2%至100%。除23号和24号染色体外，发现58个SNP在全基因组中发生了分离。本研究获得的连锁图谱为未来KU群体生长相关性状的数量性状位点（QTL）定位提供了框架。
