Linkage group correction using epistatic distorted markers in F2 and backcross populations

Sq, Xie; Jy, Feng; Zhang, Yuan-Ming

doi:10.1038/hdy.2013.127

Cited by 9 publications

(11 citation statements)

References 42 publications

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“…The same QTLs using the linkage maps of including and excluding very significantly distorted markers are marked by bold type are significantly fewer than those in OC or RC RILs. Use of fewer distorted markers in all the RILs decreases the impact of distorted marker on linkage map construction (Zhu et al 2007;Xie et al 2014), and the quality of the linkage maps increases. Second, most distorted markers are clustered.…”

Section: Discussionmentioning

confidence: 99%

“…The program MSTmap ) was used to group and order the SLAF markers. Considering the existence of marker segregation distortion, the software DistortedMap of Xie et al (2014) was used to detect marker segregation distortion. The quality of the constructed linkage maps was evaluated by the collinearity between the linkage maps in this study and the soybean reference genome, the heat map and the uniform distribution of recombination fractions on the genome.…”

Section: Linkage Map Constructionmentioning

confidence: 99%

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Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

et al. 2019

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Marker segregation distortion is a natural phenomenon. Severely distorted markers are usually excluded in the construction of linkage maps. We investigated the effect of marker segregation distortion on linkage map construction and quantitative trait locus (QTL) mapping. A total of 519 recombinant inbred lines of soybean from orthogonal and reciprocal crosses between LSZZH and NN493-1 were genotyped by specific length amplified fragment markers and seed linoleic acid content was measured in three environments. As a result, twenty linkage groups were constructed with 11,846 markers, including 1513 (12.77%) significantly distorted markers, on 20 chromosomes, and the map length was 2475.86 cM with an average marker-interval of 0.21 cM. The inclusion of distorted markers in the analysis was shown to not only improve the grouping of the markers from the same chromosomes, and the consistency of linkage maps with genome, but also increase genome coverage by markers. Combining genotypic data from both orthogonal and reciprocal crosses decreased the proportion of distorted markers and then improved the quality of linkage maps. Validation of the linkage maps was confirmed by the high collinearity between positions of markers in the soybean reference genome and in linkage maps and by the high consistency of 24 QTL regions in this study compared with the previously reported QTLs and lipid metabolism related genes. Additionally, linkage maps that include distorted markers could add more information to the outputs from QTL mapping. These results provide important information for linkage mapping, gene cloning and marker-assisted selection in soybean.

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Section: Discussionmentioning

confidence: 99%

Section: Linkage Map Constructionmentioning

confidence: 99%

Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

et al. 2019

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“…Segregation distortion is regarded as a potential evolutionary force and including these markers for linkage map construction could increase genome coverage as well as benefit QTL mapping 67 , 68 . Including SDR markers and correcting for bias led to an increase in genetic distance between distorted markers 69 . The deviation from expected Mendelian ratio shows disturbances in the transmission of genetic information from one generation to the next and can be caused by chromosome loss or rearrangements, genetic load, gametic selection, zygotic selection, or both 70 – 72 .…”

Section: Discussionmentioning

confidence: 99%

Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)

Paudel

Kannan

Yang

et al. 2018

Sci Rep

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Napiergrass (Cenchrus purpureus Schumach) is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, its utilization for breeding has lagged behind other crops due to limited genetic and genomic resources. In this study, next-generation sequencing was first used to survey the genome of napiergrass. Napiergrass sequences displayed high synteny to the pearl millet genome and showed expansions in the pearl millet genome along with genomic rearrangements between the two genomes. An average repeat content of 27.5% was observed in napiergrass including 5,339 simple sequence repeats (SSRs). Furthermore, to construct a high-density genetic map of napiergrass, genotyping-by-sequencing (GBS) was employed in a bi-parental population of 185 F1 hybrids. A total of 512 million high quality reads were generated and 287,093 SNPs were called by using multiple de-novo and reference-based SNP callers. Single dose SNPs were used to construct the first high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410 cM and a density of 1 marker per 0.73 cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.

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“…Before construction of the linkage map, the SNP markers were filtered for quality, requiring genotype calls at each SNP to have a depth of coverage of at least four reads in each individual kelp sporophyte and simultaneously excluding markers of significant segregation distortion (P < 0.05). Moreover, the segregation distortion for the SNP markers used for construction of linkage map was also examined with the software DistortedMap 34 .…”

Section: Methodsmentioning

confidence: 99%

High-density SNP-based QTL mapping and candidate gene screening for yield-related blade length and width in Saccharina japonica (Laminariales, Phaeophyta)

Wang

Chen

et al. 2018

Sci Rep

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Saccharina japonica is one of the most important marine crops in China, Japan and Korea. Candidate genes associated with blade length and blade width have not yet been reported. Here, based on SLAF-seq, the 7627 resulting SNP loci were selected for genetic linkage mapping to 31 linkage groups with an average spacing of 0.69 cM, and QTL analyses were performed to map the blade length and blade width phenotypes of S. japonica. In total, 12 QTLs contributing to blade length and 10 to width were detected. Some QTL intervals were detected for both blade length and width. Additive alleles for increasing blade length and width in S. japonica came from both parents. After the QTL interval regions were comparatively mapped to the current reference genome of S. japonica (MEHQ00000000), 14 Tic20 (translocon on the inner envelope membrane of chloroplast) genes and three peptidase genes were identified. RT-qPCR analysis showed that the transcription levels of four Tic20 genes were different not only in the two parent sporophytes but also at different cultivation times within one parent. The SNP markers closely associated with blade length and width could be used to improve the selection efficiency of S. japonica breeding.

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Linkage group correction using epistatic distorted markers in F2 and backcross populations

Cited by 9 publications

References 42 publications

Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)

High-density SNP-based QTL mapping and candidate gene screening for yield-related blade length and width in Saccharina japonica (Laminariales, Phaeophyta)

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