Allelic Diversity in MAGIC Population of Chickpea

Allelic diversity in MAGIC population of chickpea

 

Mahendar Thudi¹, Pooran M. Gaur¹, Srinivasan Samineni¹, Manish Roorkiwal¹, Emma Huang

Rajeev K. Varshney^1,2*

¹International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

²School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, Australia

*Corresponding author: r.k.varshney@cgiar.org

Molecular diversity was assessed in multi-parent advanced generation intercross (MAGIC) population of chickpea (Cicer arietinum L.). Whole- genome re-sequencing of  1136 MAGIC lines along with the parental lines generated a total of 52.02 billion clean reads (90 bp) containing 4.67 TB clean data. Alignment of sequence data on to the chickpea reference genome identified 932,172 single nucleotide polymorphisms (SNPs), 35,973 insertions and 35,726 deletions among the MAGIC lines. Average SNP density was found maximum (4.36 SNPs/Kb) on the chromosome Ca4 and minimum (0.99 SNPs/Kb) on the chromosome Ca5. On an average 86.57 % SNPs were identified in inter-genic regions. Among the SNPs in intra-genic region, the SNPs in intron were high (varied between 23,443 – 30,398 with an average of 2,609) compared to exon. LD decay varied different pseudomolecules from 0.5 Mb to 1.5 Mb. Haplotypes were determined for genomic regions responsible for some breeding traits like drought tolerance, Fusarium wilt and Ascochyta blight resistance. In summary, re-sequencing of MAGIC lines provided higher marker density in a structured population, defined haplotype groups and offered greater insights into the genome diversity for utilization in crop improvement.