Variation block-based genomics method for crop plants

Kim, Yul Ho; Park, Hyang Mi; Hwang, Tae-Young; Lee, Seuk Ki; Choi, Man Soo; Jho, Sungwoong; Hwang, Seungwoo; Kim, Hak-Min; Lee, Dongwoo; Kim, Byoung-Chul; Hong, Chang Pyo; Cho, Yun Sung; Kim, Hyunmin; Jeong, Kwang-Hwa; Seo, Min; Yun, Hong Tai; Kim, Sun Lim; Kwon, Young-Up; Kim, Wook Han; Chun, Hye Kyung; Lim, Sang Jong; Shin, Youngah; Choi, Ik‐Young; Kim, Young Sun; Yoon, Ho-Sung; Lee, Suk-Ha; Lee, Sung-Hoon

doi:10.1186/1471-2164-15-477

Cited by 16 publications

(29 citation statements)

References 41 publications

(45 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The density of the SNPs may have an inverse effect on the haplotype block length. This analysis will be useful to identify loci associated with economically important traits as reported earlier in case of soybean49. Further, the elucidation of haplotype block structure can bring important considerations for genome-wide association studies (GWAS) and genomic selection studies50.…”

Section: Resultsmentioning

confidence: 88%

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

Thudi

Chitikineni

Liu

et al. 2016

Sci Rep

View full text Add to dashboard Cite

In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.

show abstract

Section: Resultsmentioning

confidence: 88%

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

Thudi

Chitikineni

Liu

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Alongside the technical development of NGS, the recombination block-based analysis is emerging as an efficient approach for identifying soybean cultivars with high accuracy to detect genetic diversity. Recently, Kim et al (2014) determined two types of blocks by comparison of the genome sequences of six soybean cultivars: The sparse variation blocks (sVBs), which are identical or nearly identical to the reference sequence, and the dense variation blocks (dVBs), which contain many variations. The sVBs showed 6.6 times higher recombination rates than those of the dVBs, which can lead to the conservation of dVBs.…”

Section: Introductionmentioning

confidence: 99%

Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks

et al. 2017

Self Cite

View full text Add to dashboard Cite

For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, “Singang” and a recurrent parent, “Sowon” were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.

show abstract

“…If no particular segmentation pattern is specified, the reference genome FASTA file may be used to create a GFF file containing a user-defined, evenly spaced, segmentation pattern (Huang et al, 2009;Anderson et al, 2011;Prasad et al, 2013;Chen et al, 2014;Kim et al, 2014;Liu et al, 2014). The resulting GFF is then used to split the VCF files into the desired segments, as consecutive windows, sliding windows, or any arbitrary filtering from the annotation file of the reference genome such as CDS, genes, exons, introns, etc.…”

Section: The Back-endmentioning

confidence: 99%

“…To achieve this, we first calculate the average number of SNPs per sample; subsequently test whether the number of SNPs is above or below the average and then convert the sequence of the sample to the sequence of the closest parent according to the method of Kim et al (2014) and Huang et al (2009). In this way miscalls due to low genomic coverage are repaired, resulting in improved accuracy for delineated introgressed segments and a more reliable donor species identification.…”

Section: The Back-endmentioning

confidence: 99%

“…Several methods to visualize such whole-genome SNP (wgSNP) data have been presented (Posada, 2002;Martin et al, 2011;Lechat et al, 2013;Kim et al, 2014) including software packages such as VISRD (Strimmer et al, 2003), SHOREMAP (Schneeberger et al, 2009), RECOMBINE (Anderson et al, 2011), NGM (Austin et al, 2011), PARTFINDER (Prasad et al, 2013) and PHYLONET-HMM . SHOREMAP and NGM focus on identifying causal SNPs for phenotypes in segregating populations.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Introgression browser: high‐throughput whole‐genome SNP visualization

et al. 2015

View full text Add to dashboard Cite

SUMMARYBreeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.

show abstract

Variation block-based genomics method for crop plants

Cited by 16 publications

References 41 publications

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks

Introgression browser: high‐throughput whole‐genome SNP visualization

Contact Info

Product

Resources

About