First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations

Plant Biotechnology Journal
Vinay KumarRajeev K Varshney

Abstract

Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.

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Citations

Oct 21, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tinashe ChiurugwiLee T Hickey
May 26, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rachit K SaxenaRajeev K Varshney
Jun 8, 2018·Breeding Science·Kul Bhushan SaxenaRajeev K Varshney
Dec 19, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rajeev K VarshneyRachit K Saxena
Feb 18, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Abhishek BohraRachit K Saxena
Dec 18, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rachit K SaxenaRajeev K Varshney
Aug 24, 2017·Journal of Experimental Botany·Yunbi XuMichael S Olsen
Sep 3, 2018·Molecular Genetics and Genomics : MGG·Jimmy ObalaRajeev K Varshney
Oct 21, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rachit K SaxenaRajeev K Varshney
Jan 8, 2021·Journal of Plant Physiology·Mahendar ThudiRajeev K Varshney

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Methods Mentioned

BETA
array technology
genotyping
Assay
PCRs

Software Mentioned

Genome Analysis Toolkit
NGS
SnpEff
CNVnator
MAGIC
SNPhylo
bowtie2
NAM
mega
DNAML

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