Characterization of genetic diversity and population structure in wheat using array based SNP markers

Area of Science:

• Agricultural Science
• Genetics
• Plant Breeding

Background:

• Genetic diversity is vital for crop adaptation and improvement.
• India possesses rich wheat germplasm due to diverse agro-climatic conditions.
• High-throughput SNP markers are underutilized for Indian wheat germplasm characterization.

Purpose of the Study:

• To characterize the genetic diversity of Indian spring wheat germplasm.
• To utilize the 35K Axiom Wheat Breeder's Array for genome-wide SNP analysis.
• To provide insights for future wheat breeding programs.

Main Methods:

• Genotyping of 483 wheat genotypes using the 35K Axiom Wheat Breeder's Array.
• Quality filtering of 14,650 SNPs distributed across wheat genomes (A, B, and D).
• Population structure and Principal Coordinate Analysis to identify subpopulations.

Main Results:

• Identified 14,650 high-quality SNPs with good genome-wide coverage.
• Detected two distinct subpopulations (SP1 and SP2) with 98% genetic variation within subpopulations, indicating high gene flow.
• Subpopulation SP2 exhibited high genetic diversity based on Shannon's index and heterozygosity.

Conclusions:

• This study represents the largest dataset for genetic diversity analysis in Indian wheat.
• The findings offer a valuable resource for identifying quantitative trait loci (QTL) and genes.
• Results facilitate marker-assisted selection strategies for enhancing Indian wheat breeding.