Identification of growth related quantitative Trait Loci within the abalone using comparative microsatellite bulked segregant analysis

[摘要] ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is a commercially valuable mollusc and ismostly exported to the Far East. Genetics research on H. midae has increasedsubstantially since a genetic improvement programme was introduced in 2006 bycollaboration between Stellenbosch University, government and industry partners. Thedevelopment of molecular markers, QTL-mapping, gene-expression and genomemanipulations are the main focuses of the research currently being conducted. The endgoal is to create high quality and fast growing animals for the industry. The present studyfocused on the development of microsatellite markers and the detection of quantitative traitloci (QTL) affecting growth traits (shell length, shell width, wet weight) in this species. Acombination of three methods, namely selective genotyping and bulked segregant analysis(pooling analysis), single marker regression and interval mapping were used to identifyputative QTL in two full-sib families from two different farmed locations. Additional methodsand protocols were developed that can assist the industry in other molecular researchaspects. A total of 125 microsatellite loci were characterised. A total of 82 of these lociwere isolated using second generation sequencing, a first for any abalone species. Apreliminary, low-density framework linkage map was constructed containing 50 loci thatmapped to 18 linkage groups. The observed genome length was 148.72cm with coverageof ±47%. QTL analyses revealed two putative QTL for shell width and wet weight, with17% and 15% variance explained, that mapped on one linkage group in the first family andthree putative QTL, for shell length, shell width and wet weight, with 33%, 28.5% and31.5% variance explained, that mapped on one linkage group in the second family.Additional methods and protocols developed include an automated high-throughput DNAisolation protocol, a real-time PCR assay for H. midae x H. spadicea hybrid verification, atriploid verification microsatellite assay and a pre- and post-PCR multiplex setup andoptimisation protocol. Future studies focussing on QTL and marker assisted selection(MAS) should verify the QTL found in this study and also utilise additional family structuresand determine QTL-marker phase within the commercial populations.

[发布机构] Stellenbosch University