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Identification and validation of insertion–deletion polymorphisms in pigeonpea

OAR@ICRISAT

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Relation http://oar.icrisat.org/10315/
 
Title Identification and validation of insertion–deletion polymorphisms in pigeonpea
 
Creator Singh, S K
Kale, S M
Saxena, R K
Sinha, P
Parupalli, S
Suryanaraya, V
Obala, J
Sameer Kumar, C V
Varshney, R K
 
Subject Pigeonpea
Genetics and Genomics
 
Description Completely sequenced plant genomes provide scope for designing
a large number of genome wide insertion–deletion (InDel)
markers, which are useful in various aspects of crop breeding and
genetic analysis. With the objective of developing InDel markers
from pigeonpea genome, the re-sequencing data of eight MAGIC
parental lines were used to identify InDels using Dindel software.
As a result, a total of 102,181 InDels were identified. Of these
70158 InDels were found unique. The higher number of InDels
were found in intergenic (43%) followed by upstream (26%)
and downstream (24%) regions. A total of 6.93 % of Indels were
found in the genic region. Out of 70158 InDels, 2,426 (1032 Insertions
and 1394 deletions) with ≥20 bp size among different
parental lines were selected. Average distribution of selected
2426 InDels was found 220 InDels/LG with maximum number
of InDels on CcLG11 (385 InDels) and minimum number of In-
Dels on CcLG05 (70 InDels). A set of 293 InDels could assess
genetic diversity and establish phylogenetic relationships among
16 parental lines of different mapping populations. Validation of
these primer pairs on parental lines of different mapping population
resulted in higher amplification success rate (≥83%) with
almost 52.04% polymorphism rate among parental lines on 3%
agarose gel. The number of alleles per locus ranged from 2 to
9 with an average of 3.8 alleles. Further, to track the genome
of parents in complex funnel crossing scheme of pigeonpea
MAGIC population at 28-two way, 14-four way and 7-eigth way
stages, we have identified unique InDel primers for each of the
8 MAGIC parents. The result showed that InDel markers with
their high polymorphic potential in comparison to SSR markers
would be preferred candidate markers in various marker-based
applications in pigeonpea genetics and breeding.
 
Date 2017-02
 
Type Conference or Workshop Item
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/10315/1/Abstract_Book_423.pdf
Singh, S K and Kale, S M and Saxena, R K and Sinha, P and Parupalli, S and Suryanaraya, V and Obala, J and Sameer Kumar, C V and Varshney, R K (2017) Identification and validation of insertion–deletion polymorphisms in pigeonpea. In: InterDrought-V, February 21-25, 2017, Hyderabad, India.