Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer

Chun Ming Wang,Ze Yuan Zhu,Gen Hua Yue,Jian Li,Loong Chueng Lo,Grace Lin,Ping Gong,Felicia Feng

doi:10.1186/1471-2164-9-139

Abstract

BackgroundBarramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map.ResultsThis BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group.ConclusionWe have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.

Highlights

Barramundi (Lates calcarifer) is an important farmed marine food fish species
The bacterial artificial chromosome (BAC) library consisted of a total of 49,152 clones, which were manually arrayed into 128 384-well plates
Insert size distribution To examine the quality of the BAC library, the sizes of 212 BAC clones randomly picked from the library were determined

Summary

Introduction

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. Barramundi (Lates calcarifer), called Asian seabass or the giant sea perch, belonging to the family Latidae is widely distributed in the coast and freshwater of the tropical Indo-west Pacific, from the Persian Gulf to India and Northern Australia [1,2]. Because of good meat quality and relatively high market value of L. calcarifer, it has become an attractive commodity of both large and smallscale aquaculture enterprises. It is commercially cultivated in Thailand, Malaysia, Singapore, Indonesia, Hong Kong, China and Australia in both brackishwater and freshwater ponds, as well as in cages in coastal waters. Identification of genomic regions and genes (page number not for citation purposes)

Methods

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Discussion

Conclusion