Development and Validation of 50K Single Nucleotide Polymorphism (SNP) arrays (Axiom®CicerSNP Array) for accelerating Genetics and Breeding in Chickpea
Manish Roorkiwal, Scientist , ICRISAT
Deployment
of marker data for breeding application requires cost and time–effective
genotyping platform. In the case of chickpea, 70,463 high quality non redundant
SNPs were selected for developing a high-throughput SNP genotyping platform.
Further, a set of 61,174 SNPs was selected based on p-convert score = 0.3, of
which 50,590 SNPs could be tiled on Axiom®CicerSNP array. Among the selected
SNPs, 11,245 SNPs (22.23%) were found spanning across the coding regions of
3,673 different genes. On an average 6,323 SNPs/LG (Average distance of 6.86
Kb) were selected, with CaLG04 accounting for maximum (16,772 SNPs; 33.15%) and
CaLG08 for minimum (1888 SNPs; 3.73%). The developed Axiom®CicerSNP array was
used for genotyping two intra-specific chickpea recombinant inbred line viz.
ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). High success
and polymorphic rate was observed on analyzing the genotyping data, resulting
15,140 (29.93%; ICCRIL03) and 20,018 (39.57%; ICCRIL04) polymorphic SNPs.
High-density genetic maps comprising 13,679 SNPs spanning 1033.67 cM and 7,769
SNPs spanning 1076.35 cM were developed and QTLs were identified. Higher
precision and high-throughput genotyping of this array is expected to
accelerate both genetic studies and molecular breeding applications in chickpea.
|
Add to Calendar ▼2017-07-20 00:00:002017-07-21 00:00:00Europe/LondonAgriGenomics India 2017AgriGenomics India 2017 in ChandigarhChandigarhSELECTBIOenquiries@selectbiosciences.com