Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data

Mahmood, Sammina; Li, Zhaohong; Yue, Xiaopeng; Wang, Bo; Liu, Kede

doi:10.1007/s11032-016-0501-z

Cited by 14 publications

(10 citation statements)

References 43 publications

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“…Allopolyploids are known to undergo diploidization after whole genome duplication, leading to gene loss and genomic SVs (reviewed by Fu et al, 2016 ). Whole genome sequences are a valuable resource for the evaluation of SVs such as the indels (<50 bp) identified by Mahmood et al (2016) and Schmutzer et al (2015) , as well as the deletions and insertions (>50 bp) identified in the current study. The majority of SVs were found in non-coding regions although a significant number overlap genic regions, both coding and non-coding, confirming a functional role of SVs in gene effect and differentiation.…”

Section: Discussionmentioning

confidence: 91%

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

et al. 2018

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Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

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Section: Discussionmentioning

confidence: 91%

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

et al. 2018

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“…Moreover, they can amplify target fragments from mixed or highly degraded DNA samples 34 . InDel markers have been developed for several crops including cotton, rice, maize, rapeseed, cucumber etc [35][36][37][38][39][40][41] . It is clear that some polymorphic InDel markers were previously developed for genotyping of cucumber and has been applied on 6 typical cucumber germplasm 42 nonetheless; they were all resolvable on polyacrylamide gel due to the InDel sizes.…”

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confidence: 99%

Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber

Adedze¹,

Lu²,

Xia³

et al. 2021

Sci Rep

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Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.

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“…Polymorphism between the parents was also screened using previously published 212 SSRs ( Cheng et al 2009 , Xu et al 2010 , Yang et al 2012 ), and 595 in-house INDELs developed from resequencing data of 22 rapeseed cultivars ( Mahmood et al 2016 ). The 595 INDELs were evenly distributed throughout the A and C subgenomes and uniquely mapped on the reference genomes of B. napus .…”

Section: Methodsmentioning

confidence: 99%

High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (<i>Brassica napus</i> L.)

et al. 2017

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Rapeseed (Brassica napus L.) is one of the most important oil crops almost all over the world. Seed-related traits, including oil content (OC), silique length (SL), seeds per silique (SS), and seed weight (SW), are primary targets for oil yield improvement. To dissect the genetic basis of these traits, 192 recombinant inbred lines (RILs) were derived from two parents with distinct oil content and silique length. High-density linkage map with a total length of 1610.4 cM were constructed using 1,329 double-digestion restriction site associated DNA (ddRAD) markers, 107 insertion/deletions (INDELs), and 90 well-distributed simple sequence repeats (SSRs) markers. A total of 37 consensus quantitative trait loci (QTLs) were detected for the four traits, with individual QTL explained 3.1-12.8% of the phenotypic variations. Interestingly, one OC consensus QTL (cqOCA10b) on chromosome A10 was consistently detected in all three environments, and explained 9.8% to 12.8% of the OC variation. The locus was further delimited into an approximately 614 kb genomic region, in which the flanking markers could be further evaluated for marker-assisted selection in rapeseed OC improvement and the candidate genes targeted for map-based cloning and genetic manipulation.

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Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data

Cited by 14 publications

References 43 publications

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber

High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (<i>Brassica napus</i> L.)

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