Genetic improvement of clariid catfishes genome-wide association study in clarias macrocephalus and genetic characterization of its hybrid with clarias gariepinus

Name: Prapaiphan Chaivichoo

LCSH: Kasetsart University -- Dissertations. Ph.D. (Aquaculture) 2023.

Classification :.LCCS: QL637.9.S5

LCSH: Kasetsart University. -- Department of Aquaculture -- Dissertations.

LCSH: Catfishes -- Breeding.

LCSH: Catfishes -- Genetics.

LCSH: Genomics.

LCSH: Genetic markers.

Abstract: The hybrid between male North African catfish (Clarias gariepinus Burchell, 1822) and female bighead catfish (C. macrocephalus Günther, 1864) is economically important in Thailand and neighboring countries. However, there has been a lack of consideration for a genetic approach to enhance the hybrid's performance. This study aims to fill this gap by investigating the genetic components influencing the hybrid's growth performance, identifying Single Nucleotide Polymorphisms (SNPs) associated with growth traits using Genome-Wide Association Studies (GWAS) and estimating genetic parameters as well as predicting EBV based on SNPs and pedigree information in C. macrocephalus. In the first study, a partial factorial mating scheme was employed to hybridize five families each of fast- and slow-growing male C. gariepinus and female C. macrocephalus. The mating resulted in 40 full-sib families, consisting of 10 paternal half-sibs and 7 maternal half-sibs. Subsequently, the progenies were tagged by families and communally reared in two earthen ponds. Variance components for body weight (BW), total length (TL) and standard length (SL) of the hybrids were estimated using the PROC MIXED procedure of SAS 9.0. The results revealed that only the general combining ability (GCA) of male C. gariepinus (362.64 for BW, 0.25 for SL and 0.29 for TL) was significant, whereas the GCA of the female C. macrocephalus and the specific combining ability (SCA) were nonsignificant (p>0.05). These results imply that the growth performance of the hybrid depends largely on the additive genetic variation of the male parent. In the second study, individual DNA samples collected from 991 eight-month-old C. macrocephalus, representing 74 full-sib families and 31 half-sib families, were subjected to next-generation sequencing using the DArTSeq platform, resulting in 9,530 SNPs that were utilized alongside recorded phenotypic data for subsequent analysis. The analysis was performed using weighted genomic best linear unbiased prediction (wGBLUP), facilitated by the BLUPF90 family of programs. Additionally, GBLUP and PBLUP were utilized to estimate heritability and (G)EBV for the growth traits. GWAS results identified 19 markers associated with all growth traits, with the proportion of genetic variance explained ranging from 1.02% to 6.59%. Four SNP sequences were annotated to specific genes: Egl nine 2- like gene (egln2), zinc finger FYVE-type containing 21 gene (zfyve21), junctophilin 3a (jph3a), and a hypothetical protein. Prediction accuracy indicated that GBLUP enhanced the accuracy of EBV estimates as compared to the PBLUP, with accuracy ranging from 0.672 to 0.724 and prediction bias close to one. The heritability of growth traits, estimated by GBLUP, ranged from 0.29 ± 0.05 (for standard length) to 0.55 ± 0.06 (for body weight), which are higher than the heritability estimated by PBLUP.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Uthairat Na-nakorn

Role: Thesis Advisor

Name: Skorn Koonawootrittriron

Role: Thesis Co-Advisor

Created: 2023

Modified: 2025-06-26

Issued: 2025-06-26

วิทยานิพนธ์/Thesis

วิทยานิพนธ์/Thesis

application/pdf

URL: http://www.lib.ku.ac.th/KUthesis/2566/prapaiphan-cha-all.pdf

CallNumber: QL637.9.S5.P73

eng

DegreeName: Doctor of Philosophy

Level: Doctoral Degree

Descipline: Aquaculture

Grantor: Kasetsart University

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