Abstract
Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp.
Highlights
Can increase the accuracy and efficiency of selection, thereafter is an ideal mean for traits that are difficult to be improved by traditional selection
Four segregation distortion region (SDR) were detected in the map, and two of them were in LG13, which were separated by only one un-skewed marker
Linkage map is an important pre-requisite for mapping quantitative trait locus (QTL) of interested traits for a given species
Summary
Can increase the accuracy and efficiency of selection, thereafter is an ideal mean for traits that are difficult to be improved by traditional selection. Some work had been done on development of co-dominate DNA markers and linkage map construction[22,23,24]. The main purpose of our present study is to construct a high-density linkage map with only SNP markers to facilitate QTL mapping for growth related traits, such as body weight (BW), body length (BL), total length (TL), head length (HL) and body height (BH). We mapped all the reads from parents and offspring to the loci and genotyped every locus with at least 80% of progenies presented. We found 7,786 loci were polymorphic and used them in the following map construction Among these loci, 5,567 were co-dominant loci which were present in both parents. After discarding 4,463 SNPs with segregation distortion the rest 3,323 markers were used in sex-average linkage group assignment. These SDRs may be related with preferential selection and would not affect the LG Name Num of SNPs LG length(cM) Average Dist(cM) Largest Gap(cM)
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