Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

Area of Science:

• Agricultural Science
• Genomics
• Plant Breeding

Background:

• Cultivated peanut (Arachis hypogaea) is a vital food source, necessitating genetic enhancement.
• Advancements in sequencing diploid ancestors of peanut have spurred genomic resource development.
• High-throughput genotyping is crucial for accelerating genetic improvement in Arachis species.

Purpose of the Study:

• To develop a large-scale SNP genotyping array for high-throughput genotyping of Arachis species.
• To facilitate the identification of genetic markers for cultivated peanut improvement.
• To support the inclusion of new genetic diversity in peanut breeding programs.

Main Methods:

• Re-sequencing of 20 Arachis genotypes to select genome-wide single nucleotide polymorphisms (SNPs).
• Development of a 384-accession SNP array incorporating SNPs polymorphic between tetraploid and diploid species.
• Genotyping of elite cultivars to identify regions of positive selection in US runner germplasm.

Main Results:

• The SNP array successfully identified 54,564 polymorphic markers between diploid species, 47,116 between cultivated and interspecific hybrids, and 15,897 within A. hypogaea germplasm.
• An additional 1,193 markers were found to indicate tetrasomic recombination.
• Genotyping of elite cultivars revealed genomic regions under positive selection.

Conclusions:

• The developed SNP array is efficient, comprehensive, and flexible for genetic and breeding applications in Arachis.
• The findings provide insights for incorporating new genetic diversity into cultivated peanut.
• The array will aid in the development of high-resolution mapping populations for peanut improvement.