Microsatellite-centromere mapping in common carp through half-tetrad analysis in diploid meiogynogenetic families

Abstract

Gene-centromere (G-C) mapping provides insights into the understanding of the composition, structure, and evolution of vertebrate genomes. Common carp (Cyprinus carpio) is an important aquaculture fish and has been proposed to undertake tetraploidization. In this study, we selected 214 informative microsatellite markers across 50 linkage groups of a common carp genetic map to perform genecentromere mapping using half-tetrad analysis. A total of 199 microsatellites were segregated under the Mendelian expectations in at least one of the three gynogenetic families and were used for G-C distance estimation. The G-C recombination frequency (y) ranged from 0 to 0.99 (0.43 on average), corresponding to a fixation index (F) of 0.57 after one generation of gynogenesis. Large y values for some loci together with significant correlation between G-C distances and genetic linkage map distances suggested the presence of high interference in common carp. Under the assumption of complete interference, 50 centromeres were localized onto corresponding linkage groups (LGs) of common carp, with G-C distances of centromere-linked markers per LG ranging from 0 to 10.3 cM (2.9 cM on average). Based on the information for centromere positions, we proposed a chromosome formula of 2n=100=58 m/sm+42 t/st with 158 chromosome arms for common carp, which was similar to a study observed by cytogenetic method. The examination of crossover distributions along 10 LGs revealed that the proportion of crossover chromatids was overall higher than that of non-crossover chromatids in gynogenetic progenies, indicating high recombination levels across most LGs. Comparative genomics analyses suggested that the chromosomes of common carp have undergone extensive rearrangement after genome duplication. This study would be valuable to elucidate the mechanism of genome evolution and integrate physical and genetic maps in common carp.

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

“…Compared with the genetic map of Songpu mirror carp ( C. c. carpio ) [ 34 ], this map had a slightly larger size (4586.56 vs 3946.7 cM) and a higher resolution (0.57 vs 0.93 cM). On LG21 and LG26, few markers were located at the terminal region, which may be caused by the presence of centromeres [ 3 ], and/or the effect of DNA methylation. Attention should be paid to the caution of mapped markers at the terminal region and the effect of DNA methylation as this might involve in the reality and accuracy of some SNP loci.…”

“…A genetic linkage map is an essential tool in many genetics and genomics researches, such as quantitative trait loci (QTL) mapping for target traits of economic importance [ 1 ], positional or candidate gene cloning [ 2 ], construction of gene-centromere maps [ 3 ], comparative genome analysis [ 4 ] and genome assembly [ 5 ]. In most important aquaculture species, genetic maps have been constructed using amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers [ 6 ].…”

Microsatellite-centromere mapping in Japanese scallop (Patinopecten yessoensis) through half-tetrad analysis in gynogenetic diploid families

“…Genetic maps have been published for the Japanese scallop using amplified fragment length polymorphism (AFLP) and microsatellite markers (Chen et al, 2012;Xu et al, 2008); however, there is still no marker-centromere (M-C) mapping documented in the scallop species. Marker-centromere mapping estimates have been reported in many fish species such as salmonids (Lindner et al, 2000), carps (Zhu et al, 2013;Feng et al, 2015) and catfish (Poompuang and Sukkorntong, 2011). They have also been reported in several shellfish species including the Pacific oyster (Hubert et al, 2009), Pacific abalone (Nie et al, 2012), blue mussel (Besumont and Fairbrother, 1995) and Zhikong scallop (Nie et al, 2013).…”

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma

“…A genetic linkage map is a very useful tool to understand genetic architecture such as chromosome structure, segregation distortion regions, recombination rate, and recombination hotspots (Myers et al 2005; Zhu et al 2014; Guo et al 2013; Shifman et al 2006). Furthermore, it provides a framework for mapping the chromosomal location of single-gene traits and quantitative traits of interest, and helps to facilitate candidate gene cloning, and comparative genomic analysis with some genome information together (Lee et al 2005; Amores et al 2011; Feng et al 2015; Zhu et al 2013; Li et al 2015; Shao et al 2015; Wang et al 2015; Xiao et al 2015; Kanamori et al 2016). A high-density genetic map also plays an important role in assembling whole genome sequences by examining the accuracy of de novo genome assembly (Dukic et al 2016; Rhee et al 2017; Wang et al 2017).…”