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Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

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Relation http://oar.icrisat.org/9311/
http://dx.doi.org/10.1186/s12870-015-0690-3
10.1186/s12870-015-0690-3
 
Title Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)
 
Creator Thudi, M
Khan, A W
Kumar, V
Gaur, P M
Katta, K
Garg, V
Roorkiwal, M
Samineni, S
Varshney, R K
 
Subject Chickpea
Genetics and Genomics
 
Description Background: Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor
farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for
chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping
populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight,
Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole
genome re-sequencing approach.
Results: A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads,
with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype
were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide
polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome.
Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such
as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI
489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and
19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV
97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intrachromosomal
variations (ITX) and inversions (INV) respectively.
Conclusion: Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping
populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible
for economically important traits. Further, the genome-wide variations identified in the present study can be used for
developing high density SNP arrays for genetics and breeding applications.
 
Publisher Springer
 
Date 2016-01-27
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/9311/1/art%253A10.1186%252Fs12870-015-0690-3.pdf
Thudi, M and Khan, A W and Kumar, V and Gaur, P M and Katta, K and Garg, V and Roorkiwal, M and Samineni, S and Varshney, R K (2016) Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biology, 16 (10). pp. 53-64. ISSN 1471-2229