High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc)

Jie, Zhang; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Zhong, Junjun; Huang, Long; Liu, Enze

doi:10.1093/dnares/dsv003

Cited by 136 publications

(167 citation statements)

References 55 publications

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“…After the low-quality reads (quality score < 20e) were filtered out, the SLAF pair-end reads with clear index information were clustered based on sequence similarity (BLAT) [35, 36] (−tileSize = 10 –step Size = 5). Sequences with over 95% identity were grouped in one SLAF locus.…”

Section: Methodsmentioning

confidence: 99%

Construction of a high-density genetic map using specific-locus amplified fragments in sorghum

Qing-jiang

et al. 2017

BMC Genomics

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BackgroundSorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. Thus it is regarded as a model crop for energy plants. Genetic map construction is the foundation for marker-assisted selection and gene cloning. So far several sorghum linkage maps have been reported using different kinds of molecular markers. However marker numbers and chromosome coverage are limited. As a result, it is difficult to get consistent results and the maps are hard to unify. In the present study, the genomes of 130 individuals consisting an F2 population together with their parents were surveyed using a high-throughput sequencing technique. A high-density linkage map was constructed using specific-locus amplified fragments (SLAF) markers. This map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program.ResultsA high-throughput sequencing method was adopted to screen SLAF markers with 130 F2 individuals from a cross between a grain sorghum variety, J204, and a sweet sorghum variety, Keter. In the present study, 52,928 suitable SLAF markers out of 43,528,021 pair-end reads were chosen to conduct genetic map construction, 12.0% of which were polymorphic. Among the 6353 polymorphic SLAF markers, 5829 (91.8%) were successfully genotyped in the F2 mapping population. Finally 2246 SLAF markers were obtained to construct a high-density genetic linkage map. The total distance of linkage map covering all 10 chromosomes was 2158.1 cM. The largest gap on each chromosome was 10.2 cM on average. The proportion of gaps less than and/or equal to 5.0 cM was averagely 98.1%. The markers on each chromosome ranged from 123 (chromosome 9) to 315 (chromosome 4) with a mean value of 224.6, the distance between adjacent markers ranged from 0.6 (chromosome 10) to 1.3 cM (chromosome 9) with an average distance of only 0.98 cM.ConclusionA high density sorghum genetic map was constructed in this study. The total length was 2158.1 cM covering all 10 chromosomes with a total number of 2246 SLAF markers. The construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3430-7) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Construction of a high-density genetic map using specific-locus amplified fragments in sorghum

Qing-jiang

et al. 2017

BMC Genomics

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“…Importantly, reference genome sequences and polymorphism information are not necessary when this method is used. This method has been applied in many species for genetic map construction as a rapid and cost-effective strategy for high-throughput SNP and InDel discovery and genotyping181920.…”

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confidence: 99%

Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis)

Liu

Fan

Cao

et al. 2016

Sci Rep

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A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs). After binning the SLAF markers that represented the same genotype, the final linkage map of 1628.15 cM contained 2032 markers, with an average marker density of 0.80 cM. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris). Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. These results provide a foundation that will be useful for future genomic research, such as identifying QTLs for other important traits, positional cloning, and comparative mapping in legumes.

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“…However, CMD resistant loci have been described using eight molecular markers (Rabbi et al, 2014;Okogbenin et al, 2012;Lokko et al, 2005;Akano et al, 2002) that are sparsely distributed, making it impracticable to precisely associate flanking markers with CMD resistant status. High quality genome assembly and dense genetic maps are essential tools for mapping to allow identification of loci associated with traits (ICGMC, 2015;Gaur et al, 2015;Zhang et al, 2015). In soybean, for example, a high density genetic map saturated with 2500 molecular markers were developed to precisely map QTLs conferring resistance to Fusarium graminearum on 300 kb region of chromosome 8 (Acharya et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…In soybean, for example, a high density genetic map saturated with 2500 molecular markers were developed to precisely map QTLs conferring resistance to Fusarium graminearum on 300 kb region of chromosome 8 (Acharya et al, 2015). Likewise, Zhang et al (2015) developed linkage map containing 8007 markers to identify weeping trait in an ornamental woody plant Prunus mume. Such quality density maps are not be available for cassava.…”

Section: Discussionmentioning

confidence: 99%

Identification and analysis of cassava genotype TME3 bacteria artificial chromosome libraries for characterization of the cassava mosaic disease

Kuria¹,

Ateka²,

Miano³

et al. 2016

Afr. J. Biotechnol.

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Cassava is an economically important crop in sub-Saharan Africa; however, its yield potential is constrained by cassava mosaic disease (CMD) infection. Classical genetics and biotechnology are being harnessed to overcome the disease and secure yields for farmers. The CMD2 resistance locus flanked by three simple sequence repeats (SSR) markers and one sequence characterized amplified region (SCAR) marker were mapped in West African genotypes and shown to impart qualitative resistant to all species of CMGs. However, gene(s) associated with the CMD2 locus and their mode of actions remains unknown. In an effort to discover gene(s) located in CMD2 locus region, TME3 BAC collections were screened for the presence of CMD2 flanking markers. CMD susceptible and resistant cassava genotypes were found to contain 100% of the markers flanking CMD2 locus. SNPs and nucleotide deletions were identified within the marker sequences but there was no evidence of trait and marker association. All the SSR markers flanking CMD2, and the more recently characterized CMD3 loci were to be located on chromosome 12. Through BAC pools library hybridization with marker probes, 130 BACs were identified, but only 23 BACs contained at least CMD2 specific two markers. Whole BAC sequencing identified five clones that mapped to the marker regions. BAC29 assembled into a 100 kb contig and encoded tandem repeats of three full length R genes (3.5 kb) and two partial repeats. These R genes were conserved and highly expressed in CMD susceptible and CMD resistant cassava genotypes. Promoter sequences derived from R genes showed similar transient expression of GUS as 35S promoter. On cassava genome V6.1 BAC29 sequences were mapped to chromosome 16, eliminating their potential role in CMD resistant.

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High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc)

Cited by 136 publications

References 55 publications

Construction of a high-density genetic map using specific-locus amplified fragments in sorghum

Construction of a high-density genetic map using specific-locus amplified fragments in sorghum

Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis)

Identification and analysis of cassava genotype TME3 bacteria artificial chromosome libraries for characterization of the cassava mosaic disease

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